[Freesurfer] long_mris_slopes error

Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: --- SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects

[Freesurfer] Advice - best method, longitudinal vs. cross-sectional

Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a longitud

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

multiple scans/subject. > > cheers > Bruce > On Tue, 3 Jun 2014, Alexandru Hanganu wrote: > >> Hello Everyone, >> >> could someone please give us an advice about which method you consider is >> the best for our study ? >> >> we have two groups wi

[Freesurfer] Longitudinal prediction

Dear FreeSurfer Experts, How could the longitudinal analysis be performed in order to show whether a parameter at time 1 is predictive of changes in cortical thickness over time ? and can thecorresponding regions be shown in FreeSurfer ? In a statistical analysis, as we see it, we must perfo

[Freesurfer] Symposium on Parkinson’s disease, early triggers - MRI, PET, inflammation, genetics

, from an MRI, PET, inflammation, morphopathology and genetics perspectives. Early registration deadline: 1st March 2019. more details at: http://fourwav.es/neurosciences21-22mai2019 On behalf of the organizing committee, Alexandru Hanganu ___ Freesurfer

[Freesurfer] X Coordinates signs switched after Qdec

negative. Two questions: - are the p-values actually t-values ? - normally the X coordinates of the right hemisphere should be positive. Any ideas why they are negative ? Thank's a lot for any help. Best regards, Dr. Alexandru Hanganu ___ Departme

[Freesurfer] mri_surf2surf - Error

and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help. Best regards, Dr. Alexandru Hanganu

AW: [Freesurfer] mri_surf2surf - Error

Von: Doug Greve <[EMAIL PROTECTED]> An: Alexandru Hanganu <[EMAIL PROTECTED]> CC: FS Mailing List Gesendet: Dienstag, den 18. November 2008, 19:39:04 Uhr Betreff: Re: [Freesurfer] mri_surf2surf - Error did you create a subject called "average"? This is d

[Freesurfer] Statistic analysing for a mask

goal ? Thank you. Best regards, Dr. Alexandru Hanganu ___ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany. ___ Freesurfer ma

RE: [Freesurfer] Statistic analysing for a mask

Thank you Nick, and Doug for your answers. I used both "--reshape" flag and "--noreshape" flag and the results after "mri_segstats" were in both cases: . . . Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each

RE: [Freesurfer] Statistic analysing for a mask

of 3D to surface ? Thank you for your help, Alex. Von: Doug Greve <[EMAIL PROTECTED]> An: Alexandru Hanganu <[EMAIL PROTECTED]> CC: FS Mailing List Gesendet: Montag, den 8. Dezember 2008, 19:41:52 Uhr Betreff: Re: [Freesurfer] Statistic analysin

[Freesurfer] QDEC data into FSL

Hello All, Can you please tell me, when we get the results from QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we threshold the image and include it as a seed into FSL tractography ? What command line should I use ? Thank you for your help, Best regards, Alexandru

RE: [Freesurfer] QDEC data into FSL

Thank you Nick for your answer. We will try this method. Von: Nick Schmansky An: Alexandru Hanganu CC: Freesurfer Mailing List Gesendet: Donnerstag, den 11. Dezember 2008, 23:16:15 Uhr Betreff: Re: [Freesurfer] QDEC data into FSL Alexandru, I can'

AW: [Freesurfer] Statistic analysing for a mask

0.9403-0.5673 5.00 5.5673 2 1 15731 15731.0 2.39290.7417 0.8352 4.45 3.6158 Sincerely, Alex. Von: Doug Greve An: Alexandru Hanganu CC: FS Mailing List Gesendet: Montag, den 8. Dezember 2008, 19

Re: [Freesurfer] error in longitudinal stream command

External Email - Use Caution Hello Martin, I was wondering - how solved the "Unmatched" error ? In our case, this error appears for both 5.3, 6.0 and dev, on 2 different clusters. All folders exist, are filled with data and reecon-all finished without error, plus hippocampus and

Re: [Freesurfer] error in longitudinal stream command

end details? > > Best, Martin > > On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote: > > External Email - Use Caution > > Hello Martin, > > > > I was wondering - how solved the "Unmatched" error ? > > > > In our case, this er

[Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined

External Email - Use Caution Hello FreeSurfer Developers, I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since

Re: [Freesurfer] Unmatched error

External Email - Use Caution Hi, I also had this error in the past. It would be reasonable to try and log all the steps now, because I didn't manage to find out where that error was coming from. In my case - I made adjustments to my own scripts. I can take a look at your scripts,

Re: [Freesurfer] Unmatched error

External Email - Use Caution Hi, In this case, there's a list of steps, written by Martin Reuter in one of the previous answers: check that folders exist, are filled with data and reecon-all finished without error check that all folders and readable: (chmod 777 -R) check in the

[Freesurfer] Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years

and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and

Re: [Freesurfer] FreeSurfer 7.1.1 is released

External Email - Use Caution Hi Freesurfer, can't find if this was reported. This refers to freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551. seems that in the new 7.1.1 version the required license file is located at FRESURFER_HOME/license.txt (instead of previous version

[Freesurfer] Postdoc position: Neuroimaging, University of Montreal, Canada, 2 years

e send applications (Cover letter, CV, names of 3 references including current supervisor and github repository) to: Alexandru Hanganu: alexandru.hang...@umontreal.ca (Primary Supervisor) and Oury Monchi: oury.mon...@ucalgary.ca (Co-Supervisor) ___ Free

[Freesurfer] Compare left vs right hemisphere

Dear Doug, There´s a message in the list from Dec. 2008 about interhemispheric comparison, and you said there wasn't any good way to do this. Is there some new method included in FS 5.0 for right vs left hemisphere comparison ? Thanks. Sincerely, Alex. * * _

[Freesurfer] cluster and FS new-version adaptation

Dear Freesurfer experts, 1) How many simultaneous processing can be done on a cluster ? I did 20 analysis at the same time, and it worked. They all finished without error. (didn't find this question on the list) 2) In order to adapt the previous subject analysing to the new FS-5.1, must I use the

[Freesurfer] QDEC thickness data to table

Dear Freesurfer experts, In the QDEC plot there is the possibility to view cortical thickness for each subject in a specific region. Is there a possibility to make an automatic table of all these thickness data ? In a previous question, the answer was to use a script: ===