Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

ral ventricle is not really concerning to me. Oftentimes there are differences on border voxels, and border voxels can easily make 5% or more of a structure. If you compare them visually, do you see big differences? On 9/12/2022 7:41 AM, Bernardoni, Fabio wrote: External Email - Use

[Freesurfer] volume differences between longitudinal and crosssectional preprocessing

External Email - Use Caution dear freesurfer experts comparing the results of longitudinal vs. crosssectional preprocessing for single time point participants I have noticed that there are some quite substantial differences (>5% for some sub cortical regions). I wonder whether

Re: [Freesurfer] lGI value aberrantly high, again

gain Sorry, the developer of this program has moved on in her career so we have no one to support it anymore. We maybe looking at it again in the next year or so. On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote: > External Email - Use Caution > > Dear all > > as some oth

[Freesurfer] lGI value aberrantly high, again

External Email - Use Caution Dear all as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWS

Re: [Freesurfer] problem with mris_compute_lgi

203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Gesendet: Mittwoch, 30. Juni 2021 14:07:34 An: freesurfer mailing list Betreff: [Freesurfer] problem with mris_compute_lgi External Email - Use Caution Dea

[Freesurfer] problem with mris_compute_lgi

External Email - Use Caution Dear FS experts, when running mris_compute_lgi, the make_outer_surface step produces an error: >> reading filled volume... /bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81860215899812157.lo

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

ed E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Gesendet: Freitag, 14. Mai 2021 17:35:25 An: freesu

Re: [Freesurfer] memory allocation error

rfer-boun...@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Gesendet: Donnerstag, 20. Mai 2021 11:17:05 An: Freesurfer support list Betreff: Re: [Freesurfer] memory allocation error External Email - Use Caution dear Andrew, I was allowing 8, 16, ~36GB of memory in different runs,

Re: [Freesurfer] memory allocation error

f of Bernardoni, Fabio Date: Tuesday, May 11, 2021 at 4:22 AM To: freesurfer mailing list Subject: Re: [Freesurfer] memory allocation error External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medi

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

r. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: Bernardoni, Fabio Gesendet: Freitag, 14. Mai 2021 17:28:18 An: freesurfer@nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] how to visualize statistical maps in FS7.1? Dear Greve, thanks for

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

esurfer] how to visualize statistical maps in FS7.1? your tksurferfv command line is wrong On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote: > External Email - Use Caution > > Dear Freesurfers > > I recently moved to FS7.1 and I was trying to reproduce my workflow I had

[Freesurfer] how to visualize statistical maps in FS7.1?

External Email - Use Caution Dear Freesurfers I recently moved to FS7.1 and I was trying to reproduce my workflow I had with FS5.3. To visualize statistical maps, I had always used tksurfer. It seems, however, it is no longer maintained. When I launch it it fails to find out

Re: [Freesurfer] memory allocation error

203 145 03113 Von: Bernardoni, Fabio Gesendet: Dienstag, 11. Mai 2021 10:20:19 An: freesurfer mailing list Betreff: AW: memory allocation error Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described

Re: [Freesurfer] memory allocation error

External Email - Use Caution Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1Ip5HtCg9MqyghYHl20NFxCMImoJoShIH1y6ytQEK2tKtD13Oz0AIBueggTl_ahZFc6uNPUz7V5A3

Re: [Freesurfer] how does the content of the curv files compare to that of smoothwm.H.crv

Dear Bruce, thanks a lot for your answer. I am still a bit confused. I followed your suggestion to use msris_curvature to compute the curvature on the white surface (unsmoothed) instead of on smoothwm: mris_curvature -w -a 10 $subj/surf/lh.white mris_preproc -s $subj --target fsaverage --hemi l

[Freesurfer] freesurfer preproc output

Dear all, after running a freesurfer preprocessing, in each subject subdirectory, the following files are produced: lh.avg_curv lh.curv lh.curv.pial (and the analogue for the right hemisphere) what is the content of these files? sure, I can guess they represent the local curvature. but

[Freesurfer] gyrification and longitudinal processing

dear freesurfer enthusiasts, does it makes sense to compute the local Gyrification Index (lGI) on longitudinally preprocessed subjects? thanks fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-5245 Fax

[Freesurfer] lme_realizedPower

Dear Freesurfers, I have used an LME model to describe the evolution of cortical thickness in a patient group during therapy and to compare it, at the end of the therapy, with an HC group. An F-test, using the lme_F function gives no significant difference. Now I would like to understand to whi

[Freesurfer] how to choose the best random effect in LME models

Dear Freesurfer Users, I am trying different LME models to describe the time evolution of cortical thickness in anorexia patients. The LME tools provide a function (lme_mass_LR) to test whether a model with q+1 random effects is better (fits the data better) than one with q random effects, eg w

[Freesurfer] Sniffing dialect of qdec table in asegstats2table

Dear all, I am trying to perform a longitudinal lme analysis using freesurfer 5.3.0. For qdec tables with many columns the asegstats2table (and similarly aparcstats2table) commands fail with error message: asegstats2table --qdec-long ./qdec/long.qdec.table.dat --delimiter space --meas volume

Re: [Freesurfer] Problem with freeview

Dear Ruopeng, I didn't install it myself, but I guess it is a stable one. Are you suggesting the timecourse option might simply not be available in the stable version? thanks fabio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] Problem with freeview

Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.p