[Freesurfer] create a table from measures under multiple subjects

Hi Freesurfers, I calculated the thicknesses of a cluster for some subjects, and each of the measure was saved under each subject' s folder. How to create a table containing all the measures? What is the command? Thanks, Yawu ___ Freesurfer mailing list F

Re: [Freesurfer] QdecGlmDesign::Create: zero factors!

Hi Doug, Sure. I have attached a screenshot of the design tab as well as the terminal output, mydata.table.dat/Gender.levels/Group.levels files. Many thanks in advance. Clare From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Defining ROI and Finding the Cortical Thickness

Dear Douglas, To define my new label, I choose the ROI section and choose "New ROI". Then I save it, but it doesn't work properly. In addition, I cant save it on fsaverage. Best Regards, Mahtab. On 12 May 2016 at 22:08, Douglas N Greve wrote: > > > On 05/12/2016 05:46 AM, Mahtab Farahbakhsh w

[Freesurfer] Error with mris_anatomical_stats

Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? Best Regards, Mahtab. ___ Freesurfer

Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 29

Dag Jolijn, Gegenereerd! En ik heb gezien dat nr 13136 wm_lh_g_temp_sup_plan_tempo ertussen staat! (output linux) :) Groetjes, Caroline -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens freesurfer-requ...@nmr.mg

Re: [Freesurfer] Error with mris_anatomical_stats

Hi Mahtab can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is? cheers Bruce On Thu, 19 May 2016, Mahtab Farahbakhsh wrote: Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an e

Re: [Freesurfer] WM Hyperintensities

Hi Elijah no, we don't have the resources to document, test, distribute and support it. I wish we did sorry Bruce On Wed, 18 May 2016, Elijah Mak wrote: Hi Martin, I am also following this thread with interest. Is that multi-modal prototype

Re: [Freesurfer] matlab crashes on selxavg

sounds like you are running out of memory, no? On Wed, 18 May 2016, S.V.Shepherd [work] wrote: Hello, When running more than 3 analyses in parallel in FreeSurfer 5.3, I am getting matlab crashes. Mathworks has politely declined to provide support unless I can replicate outside FsFAST. The er

Re: [Freesurfer] Error with mris_anatomical_stats

Dear Bruce, This is the input command and the output that I get: bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Appl

[Freesurfer] Help with error in mkcontrast-sess command

Hi Freesurfers I am doing FSFAST with my own data and have a problem. After I run mkanalysis-sess command succesfully, I try to run mkcontrast-sess command but I get an error during the process. The text in my terminal window is the following: root@usuario2:/home/usuario2... mkcontrast-sess -anal

Re: [Freesurfer] matlab crashes on selxavg

Does it always die like that? It may be out of memory. On 05/18/2016 01:50 PM, S.V.Shepherd [work] wrote: > Hello, > > When running more than 3 analyses in parallel in FreeSurfer 5.3, I am > getting matlab crashes. Mathworks has politely declined to provide > support unless I can replicate outsi

Re: [Freesurfer] The results of your email commands

I've refreshed those links On 05/18/2016 10:44 PM, Dave Yas wrote: > Dear Doug, > > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of > -autorecon2. > I saw your answer for others about this Q before and i know how to > solve this *IF* i was able to access to the links you pos

Re: [Freesurfer] create a table from measures under multiple subjects

How did you create the measures? If with mris_anatomical_stats, then use can use aparcstats2table On 05/19/2016 03:06 AM, Liu Y wrote: > Hi Freesurfers, > I calculated the thicknesses of a cluster for some subjects, and each > of the measure was saved under each subject' s folder. How to create

Re: [Freesurfer] QdecGlmDesign::Create: zero factors!

from the snap shot it does not look like you have selected any factors. Try clicking on and highlighting Group, for example On 05/19/2016 04:52 AM, Clare Loane wrote: > Hi Doug, > > Sure. I have attached a screenshot of the design tab as well as the terminal > output, mydata.table.dat/Gender.lev

Re: [Freesurfer] Error with mris_anatomical_stats

please send the command line and all terminal output On 05/19/2016 05:50 AM, Mahtab Farahbakhsh wrote: > Dear FreeSurfer, > > I have a problem when I use mris_anatomical_stats. It gives me an > error saying that it couldn't read the input volume which is the > wm.mgz file. would you please help

Re: [Freesurfer] Help with error in mkcontrast-sess command

you can get that function from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mkcontrast2m.m copy it to $FREESURFER_HOME/fsfast/toolbox On 05/19/2016 10:55 AM, José Paredes Pacheco wrote: > Hi Freesurfers > > I am doing FSFAST with my own data and have a problem. After I run

Re: [Freesurfer] Error with mris_anatomical_stats

The second one is a valid command (1st is not). What is the full path to the wm.mgz file that is in your anlayzed data? On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote: > Dear Bruce, > > This is the input command and the output that I get: > > bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA4

Re: [Freesurfer] Error with mris_anatomical_stats

Dear Douglas, The wm.mgz is in the mri folder so it's in: Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz. Best Regards, Mahtab. Sent from myMail for iOS Thursday, May 19, 2016, 16:19 +0100 from gr...@nmr.mgh.harvard.edu : >The second one is a valid command (1st is not). Wh

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

Hi Doug, No that’s not how I usually store my files- I have a folder for the particular study that I am working on then the dicoms for each subject in that study are stored in individual subject folders within the study folder. I got a chance to look around the recon-all logs this morning for a

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

yea, can you post the log file of both the successful and failing runs? On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > Hi Doug, > > No that’s not how I usually store my files- I have a folder for the > particular study that I am working on then the dicoms for each subject > in that study are st

Re: [Freesurfer] matlab crashes on selxavg

It happens when I run more than 3-4 analyses at once. It appears to be sensitive to other instances of Matlab being open. however, I don't see clear evidence I'm memory limited. for example, I'm currently running four selxavg in parallel, along with a separate melodic analysis. One more would cause

Re: [Freesurfer] QdecGlmDesign::Create: zero factors!

Hi Doug, Thanks, I have done as you suggested but I am still getting an error. I have attache the terminal output but also paste the error below: From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N

Re: [Freesurfer] QdecGlmDesign::Create: zero factors!

Hi Doug, Thanks, I have done as you suggested but I am still getting an error. I have attached the terminal output but also paste the error below: Data table loading completed successfully. SUBJECTS_DIR is '/Users/clareloane/Desktop/

Re: [Freesurfer] matlab crashes on selxavg

sorry, I have no idea On 05/19/2016 11:35 AM, S.V.Shepherd [work] wrote: > It happens when I run more than 3-4 analyses at once. It appears to be > sensitive to other instances of Matlab being open. however, I don't > see clear evidence I'm memory limited. for example, I'm currently > running f

Re: [Freesurfer] QdecGlmDesign::Create: zero factors!

do you have permissions to create a folder in that location? Try it from the terminal to see On 05/19/2016 11:38 AM, Clare Loane wrote: > Hi Doug, > > Thanks, I have done as you suggested but I am still getting an error. > I have attached the terminal output but also paste the error below: > > ==

Re: [Freesurfer] Freesurfer

Hi Gaurang, Can you send me this whole subject case via our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ I can take a look and get back to you. -Ani On 05/18/2016 05:29 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: > The way I made the changes was that I followed the following tutorial

Re: [Freesurfer] Help with error in mkcontrast-sess command

Thanks you Mr.Douglas. It helps me a lot. Now, I have got a new error during the selxavg3-sess command: ERROR: TR mismatch between analysis and data analysis TR = 3, data TR = 3000 The correct TR is 3 (like I wrote on mkanalysis command), but I don't know where is the data TR of 3000 or why it ha

[Freesurfer] Estimation of FWHM on surface.

Estimation of FWHM on surface. Dear Ladies and Gentlemen most likely Dr. Sereno, I would like to estimate the FWHM of cortical thickness of single subjects that have been brought into fs_average space using spherical alignment. I have crated my own matlab routine to do so but some problems remai

Re: [Freesurfer] Brainmask edit error

Hi Sabrina it's tough to tell from just the 2 slices. If you upload the subject one of us will take a look, but it may not be possible to get good surfaces with that extensive a stroke cheers Bruce On Wed, 18 May 2016, Sabrina Yu wrote: Hello,  I'm having problems with regenerating the s

Re: [Freesurfer] Error with mris_anatomical_stats

Hi Mahtab the mris_anatomical_stats help says: mris_anatomical_stats [options] [] . . . -f table output to tablefile (different format than -b). Must use-a or -l options to spec input. . . . so you are specifycing the name of the table as "anon", the n

Re: [Freesurfer] The results of your email commands

Thanks a lot. 😊 Does the snowleaopard version work on El Capitan? So by replacing the version already found in bin/mrisegstats, with the leopard one after Chomd +x, it should work? I thought i would get a link for something like mri_segstats.ElCapitan? Yas > To: freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] create a table from measures under multiple subjects

Dear Douglas, I used mri_segstats --annot to create the measures. If aparcstats2table works, how to let the program know which subjects, which path, and which file should use? Yawu On Thu, May 19, 2016 at 6:08 PM, Douglas N Greve wrote: > How did you create the measures? If with mris_anatomical