[Freesurfer] asegstats2table for all subjects in the directory

Hi Freesurfer experts, I wonder if there is a way of extracting the stats for all patients in my last run at the same time. I have around 120 observations and the asegstats2table syntax works in such a way that all the patients names should be listed: asegstats2table --subjects 004 021 040 067 08

[Freesurfer] mkdir error when running FS 6.0 hippocampal segmentation

Dear Dr. Eugenio Iglesias and FreeSurfer developers, Thank you for the development of this very useful segmentation tool! When I try to run FreeSurfer 6.0's hippocampal segmentation on our computing cluster, I get the following error: "error using mkdir; Permission denied". I am not sure which d

[Freesurfer] 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. (fwd)

FYI: this is a great program for PhD students and postdocs. -- Forwarded message -- Date: Wed, 20 Jan 2016 17:09:55 +0100 From: Christian ROUX To: ROUX Christian Subject: 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 1

Re: [Freesurfer] tutorial assistance

The error message states "cannot find /buckner_data/tutorial_subjs/group_analysis_tutorial". That looks to me like you havent set the TUTORIAL_DATA environment variable properly. Please see the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data also this page might he

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

As the error message says, you can only have two levels. With 3 levels, you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki. On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote: > Thank you for the reply D

Re: [Freesurfer] Regressing out various categorical variables

your classes are right. What are you trying to test with your contrast matrix? On 01/20/2016 05:33 AM, Erik Lindberg wrote: > Dear Freesurfers, > > I am running a design in which I want to correct for a number of > categorical variables: diagnosis, gender and apoe status and one > continuous va

Re: [Freesurfer] Freesurfer and Google Drive

Thank you! Ankita On Thu, Jan 21, 2016 at 9:41 AM Douglas N Greve wrote: > About 400MB > > > On 01/21/2016 12:18 PM, Arindam Chatterjee wrote: > > Thank you Bruce! How much total space is needed per study? > > > > Ankita > > > > On Thu, Jan 21, 2016 at 9:15 AM Bruce Fischl > > mailto:fis...@nmr

Re: [Freesurfer] tutorial assistance

to help us help you, please read our link about how to report a bug here surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks! On 01/19/2016 05:31 PM, Jasmin Alves wrote: > > Hello again freesurfer team, > > While running through the group analysis tutorial, on step "previously > cached (qcac

Re: [Freesurfer] Hippocampal subfields

Thanks Eugenio. On Thu, Jan 21, 2016 at 5:56 AM, Eugenio Iglesias wrote: > Hi Alan, > If you only want volumes, you can use quantifyHippocampalSubfields.sh. If > you want to use the segmentations for something else (eg building ROIs for > functional or diffusion), then you need to look into the

Re: [Freesurfer] Analyze to nii convertor

No, try FSL On 01/21/2016 10:08 AM, Mahmoudi, Fariborz wrote: > Hi Bruce, > > The problem is solved by adding .img extension to input file name, but I have > a new problem. The origin of the output file is not zero. Is there any switch > for > tuning the origin. My actual command line is: > > /u

Re: [Freesurfer] Freesurfer and Google Drive

About 400MB On 01/21/2016 12:18 PM, Arindam Chatterjee wrote: > Thank you Bruce! How much total space is needed per study? > > Ankita > > On Thu, Jan 21, 2016 at 9:15 AM Bruce Fischl > mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > Hi Ankita > > if you can't fit the input image then you

[Freesurfer] Crashing with Fedora 23

Hi List, We just upgraded our Linux Box to Fedora 23 and installed csh so recon-all would run, yet we’re still getting crashed analyses. Here is the error from my recon-all.error file: -- SUBJECT 2_03T_N12_12_18441 DATE Thu Jan 21 16:20:16 GMT 2016 USER dsbarron HOST

Re: [Freesurfer] Freesurfer and Google Drive

Thank you Bruce! How much total space is needed per study? Ankita On Thu, Jan 21, 2016 at 9:15 AM Bruce Fischl wrote: > Hi Ankita > > if you can't fit the input image then you definitely won't be able to fit > the output of recon-all. In general if the input is unix-readable then > you should b

Re: [Freesurfer] Freesurfer and Google Drive

Hi Ankita if you can't fit the input image then you definitely won't be able to fit the output of recon-all. In general if the input is unix-readable then you should be ok cheers Bruce On Thu, 21 Jan 2016, Arindam Chatterjee wrote: Hello Freesurfer experts,Does anyone have experience runni

[Freesurfer] Freesurfer and Google Drive

Hello Freesurfer experts, Does anyone have experience running freesurfer on a mac, pointing to images stored on Google Drive? Due to space issues on disk, I was trying to take that approach, but when I run recon-all pointing to the image stack, I get errors - and it says "For more details, see the

[Freesurfer] Posterior Probability file for Hippocampal subfields segmentation

hi, FreeSurfer experts, I have a question about the new hippocampal subfields segmentation tool in FS 6.0. I wonder if there is an option to generate the posterior probability file like "posterior_right_CA1.mgz" generated in FS 5.3. Thanks, Xinyang __

Re: [Freesurfer] Analyze to nii convertor

Hi Bruce, The problem is solved by adding .img extension to input file name, but I have a new problem. The origin of the output file is not zero. Is there any switch for tuning the origin. My actual command line is: /usr/local/freesurfer/bin/mri_convert -i ./FLAIR_Sample.img -it analyze -ot nii

Re: [Freesurfer] Analyze to nii convertor

Hi Fari we need the full command line and screen output in order to help you. cheers Bruce On Thu, 21 Jan 2016, Mahmoudi, Fariborz wrote: Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command: mri

[Freesurfer] segmentation fault with mri_label2vol

Hello Freesurfer list, I have several different surface labels that I am converting into volume regions-of-interest in white matter. For 2 out of 11 participants, one of the labels will not convert. My command has worked for these two participants with all other labels that I've tried. I have no t

Re: [Freesurfer] HippocampalSubfields only generates lh

Sorry, it wasn't clear from the previous email whether the left hemi had completed or not. Can you please send me the recon-all log file? Cheers, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/leg

Re: [Freesurfer] HippocampalSubfields only generates lh

Yes they were. > On Jan 21, 2016, at 06:14, Eugenio Iglesias wrote: > > Hi Jiook, > the log file says that the analysis of the left side did complete. Were the > output files written? > Cheers, > Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcb

Re: [Freesurfer] HippocampalSubfields only generates lh

Hi Jiook, the log file says that the analysis of the left side did complete. Were the output files written? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "J

Re: [Freesurfer] Hippocampal subfields

Hi Alan, If you only want volumes, you can use quantifyHippocampalSubfields.sh. If you want to use the segmentations for something else (eg building ROIs for functional or diffusion), then you need to look into the mgz segmentation files. Cheers Eugenio Juan Eugenio Iglesias Postdoctoral researc