Print

Print
Hi Michael and Anderson,
Of course, the problem turned out to be at my end, I think. The reason I needed to separate the CIFTI files was to convert rows to columns. Since I didn’t put a design matrix in the simple command, I didn’t get an error. When I tried to reproduce my problem, but using the design matrix, I got an error. But PALM read the CIFTI files in just fine. Still learning about CIFTI files.
Sorry for the false alarm,
Sally

On Dec 15, 2016, at 5:01 AM, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Sally,
Indeed, PALM should now be reading CIFTI files directly, with no need for -cifti-separate. Please let us know...
Thanks.
All the best,
Anderson


On 14 December 2016 at 14:31, Harms, Michael <[log in to unmask]> wrote:

Hi Sally,
We had PALM working with dscalar.nii files in a test that we just ran
recently, so there should be no need to go the more laborious
-cifti-separate route.  So, if you could help us by providing your actual
command input to PALM, and testing those options that Anderson suggested,
that would be appreciated.

cheers,
-MH

--
Michael Harms, Ph.D.

-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: [log in to unmask]




On 12/14/16, 6:09 AM, "FSL - FMRIB's Software Library on behalf of
Durgerian, Sally" <[log in to unmask] on behalf of [log in to unmask]> wrote:

Thanks Anderson,
After I sent the email I tried using -cifti-separate to get metric files.
With them as input, PALM worked as expected.
Sally

wb_command -cifti-separate data.32k_fs_LR.dscalar.nii COLUMN \
-metric CORTEX_LEFT data.32k_fs_LR_L.func.gii \
-metric CORTEX_RIGHT data.32k_fs_LR_R.func.gii

On Dec 14, 2016, at 2:21 AM, Anderson M. Winkler
<[log in to unmask]<mailto:[log in to unmask]>> wrote:

Hi Sally,

Indeed, this is a simple case -- a one-sample t-test -- and it should go
smoothly. The step where you say it hangs (when it generates the 200
sign-flips) isn't one what would cause difficulties. Nonetheless, could
you try again adding the options "-cmcx" and "-cmcp"?

Thanks.

All the best,

Anderson


On 13 December 2016 at 19:03, Durgerian, Sally
<[log in to unmask]<mailto:sallyd@mcw.edu>> wrote:
Hello Anderson,
Thank you for all the work you’ve done on PALM. I had it working for some
nifti data files, but when I tried a really simple case with CIFTI files,
matlab seemed to hang up before completing any of the randomizations/sign
changes. It doesn’t seem like such a difficult design that it would take a
long time. Do you have any idea what the problem might be?
Your help is much appreciated,
Sally

Here is what I see in the matlab window (and then I can wait for hours and
not see anything more).
Running PALM alpha102 using MATLAB 8.3.0.532 (R2014a) with the following
options:
-i data.32k_fs_LR.dscalar.nii
-accel tail
-n 200
-nouncorrected
Found FSL in /usr/share/fsl/5.0 #(note - this is version 5.0.8)
Found HCP Workbench executable in
/usr/share/workbench/bin_linux64/wb_command #(this is version 1.2.3)
Reading input 1/1: data.32k_fs_LR.dscalar.nii
Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 1.769 seconds.
Number of possible sign-flips is exp(41181.3) = 2^59412.
Generating 200 shufflings (sign-flips only).

Here is information about the input file:
Name:                     data.32k_fs_LR.dscalar.nii
Type:                     Connectivity - Dense Scalar
Structure:                CortexLeft CortexRight
Data Size:                7.37 Megabytes
Maps to Surface:          true
Maps to Volume:           false
Maps with LabelTable:     false
Maps with Palette:        true
All Map Palettes Equal:   true
Map Interval Units:       NIFTI_UNITS_UNKNOWN
Number of Maps:           31
Number of Rows:           59412
Number of Columns:        31
Volume Dim[0]:            0
Volume Dim[1]:            0
Volume Dim[2]:            0
Palette Type:             Map (Unique for each map)
CIFTI Dim[0]:             31
CIFTI Dim[1]:             59412
ALONG_ROW map type:       SCALARS
ALONG_COLUMN map type:    BRAIN_MODELS
   Has Volume Data:      false
   CortexLeft:           29696 out of 32492 vertices
   CortexRight:          29716 out of 32492 vertices

Map   Minimum   Maximum    Mean   Sample Dev   % Positive   % Negative
Inf/NaN   Map Name
 1     0.343     4.798   1.562        0.175      100.000        0.000
   0   sub01
 2     1.323     3.684   2.049        0.224      100.000        0.000
   0   sub02
...
31     0.602     4.024   2.048        0.261      100.000        0.000
   0   sub31


Sally Durgerian
Neurolab G2415
Medical College of Wisconsin
8701 W. Watertown Plank Rd.
Milwaukee WI 53226


________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.