[Freesurfer] R: Error first step FS-FAST

Thank you very much. I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but the error persist. Stefano Messaggio originale Da: std...@virgilio.it Data: 7-gen-2015 11.14 A: Ogg: [Freesurfer] Error first step FS-FAST Hi list, I'm running FS-FAST. After this command

[Freesurfer] R: Re: R: Error first step FS-FAST

How can I check whether it is executable? Thanks, Setafno Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 7-gen-2015 22.51 A: Ogg: Re: [Freesurfer] R: Error first step FS-FAST And is it executable? On 01/07/2015 04:35 PM, std...@virgilio.it wrote: > > Thank you very much. > >

[Freesurfer] R: Re: R: Re: R: Error first step FS-FAST

-rwxr-xr-x 1 root wheel 60776 Jan 29 2013 #trac-all# -rw-r--r--@ 1 Stefano staff 3985520 Jan 7 21:21 3dvolreg.afni ls -l mris_register mris_register.cls: mris_register.c: No such file or directory -rwxr-xr-x 1 root wheel 7351544 May 14 2013 mris_register Thanks, Stefano

[Freesurfer] R: R: Re: R: Re: R: Error first step FS-FAST

I have also installed AFNI as advise in http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37796.html but I did not resolved the problem. Stefano Messaggio originale Da: std...@virgilio.it Data: 8-gen-2015 0.25 A: Ogg: [Freesurfer] R: Re: R: Re: R: Error first step

[Freesurfer] R: R: R: Re: R: Re: R: Error first step FS-FAST

Porbably I have resolved by chmod +x 3dvolreg.afni Messaggio originale Da: std...@virgilio.it Data: 8-gen-2015 12.45 A: , Ogg: [Freesurfer] R: R: Re: R: Re: R: Error first step FS-FAST I have also installed AFNI as advise in http://www.mail-archive.com/freesurfer%40nmr.mgh.h

[Freesurfer] fcseed-sess - segmentation fault

Hi list, I'm running FAST on resting state data. After fcseed-config -segid 9 -fcname L_Thalamus.dat -fsd rest -mean -cfg mean.L_Thalamus.config and fcseed-sess -s Sess01 -cfg mean.L_Thalamus.config gives this error: Loading /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.

[Freesurfer] selxavg3-sess

Hi list, the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis produces this error. rawfunc2surf-sess completed Started at Sun Jan 11 00:50:53 CET 2015 Ended at Sun Jan 11 00:50:54 CET 2015 preproc-sess done -

[Freesurfer] functional connectivity analysis

Hi list,I'd like to perform functional connectivity analysis between thalamus and whole cortex. I have two groups (control and disease) and I' d like also to assess between groups differences.I'm performing these steps. Please, could you check if these are corrected and could you respond to some

[Freesurfer] R: Re: functional connectivity analysis

Thank you very much. I have looked -mcreg in http://freesurfer.net/fswiki/FsFastFunctionalConnectivityWalkthrough Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 13-gen-2015 20.55 A: Ogg: Re: [Freesurfer] functional connectivity analysis Mostly looks ok to me, exce

[Freesurfer] R: Fwd: fcseed-sess - segmentation fault

Hi list I'm running preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run fcseed-config -segid 10 -fcname L_Thalamus.dat -fsd rest -mean -cfg mean.L_Thalamus.config Create nuisance variables:fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.configfcseed-sess -s

[Freesurfer] eTIV correction and registration in common space

Hi list,please, I have two questions:a) subcortical volume correction in cross-sectional studies could be done by using total GM as covariate instead of eTIV?b) relatively to group subcortical analysis in cross-sectional studies, the anatomical images should be necessarily transformed in common

[Freesurfer] eTIV correction and registration in common space

Hi list,please, I have two questions:a) subcortical volume correction in cross-sectional studies could be done by using total GM as covariate instead of eTIV?b) relatively to group subcortical analysis in cross-sectional studies, the anatomical images should be necessarily transformed in commo

[Freesurfer] To visualize contribute of each subject in FS-FAST

Hi,I'm using FS-FAST for seed based connectivity analysis.I'd like to visualize the results for each subject in a plot as for qdec.Is it possible? If no, there is an alternative interface to visualize the contribute of each subject in each vertex/region?Thank you very much in advance. Stefano

[Freesurfer] isxconcat-sess problem

Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast L_Tha

[Freesurfer] R: Re: isxconcat-sess problem

Thank you very much. I have resolved Sess49 (--s) error but the "ERROR: Flag —s unrecognized" is still remained. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 31-mar-2015 18.07 A: Ogg: Re: [Freesurfer] isxconcat-sess problem Not sure what is going wrong with the 1st

[Freesurfer] R: Re: R: Re: isxconcat-sess problem

No, do you think that a folder is lacking (please see below)?Thanks Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 3-apr-2015 7.34 A: Ogg: Re: [Freesurfer] R: Re: isxconcat-sess problem do you have another double dash (--s) in the command line?

[Freesurfer] Visualization FS-FAST results in graphs

Hi list, I'm performing the FS-FAST for functional connectivity analysis on two groups. I'm using tkmedit to visualize the results. Is possible to load a scatter plot which describes the values of each subject for each selected voxel? e.g. I'd like to verify the presence of outliers.Scatter plot

[Freesurfer] FS-FAST subcortical mni305

Hi, I'm performing FS-FAST for functional connectivity analysis.I have performed all step for cortical labels.Now, I'd like to perform the analysis for subcortical structure.Which are the correct lines? Using preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run for e

[Freesurfer] Segmentation of hippocampal subfields version 6.0

hi list, where can I download the new version 6.0 of hippocampal subfields segmentation? And in general the new FS version 6.0? Thanks Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

[Freesurfer] R: Re: Segmentation of hippocampal subfields version 6.0

Thanks. The new version will involve also changes in the measure of perirhinal and parahippocampus? Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 15-mag-2015 15.31 A: , "Freesurfer support list" Ogg: Re: [Freesurfer] Segmentation of hippocampal subfields version 6.0

[Freesurfer] mni305 volume-based analysis

Hi list, I'm configuring mkanalysis-sess to configure an analysis for FC data by FS-FAST. No problem for cortical label: mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcex

[Freesurfer] Hippo-subfields visualization

Hi list, I'm using version 5.3 and I have performed hippo-subfields analysis. A- I'd like to visualize the mask of each subfield on the T1. In subid/mri, I run the command line above: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_

[Freesurfer] R: Re: Hippo-subfields visualization

Thanks Eugenio. Point A is resolved: some typos in line command.But, I do not found the label of perirhinal in aparc+aseg.Is possible to visualize the enthorhinal, perirhinal and parahippocampus on a surface? Stefano Messaggio originale Da: e.igles...@bcbl.eu Data: 20-mag-2015 23.05 A:

[Freesurfer] R: Re: R: Re: Hippo-subfields visualization

Thanks, I have resolved for tksurfer. However, in freeviewer I'm not able visualize correctly the labels of perirhinal and entorhinal in aparc+aseg. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 21-mag-2015 21.48 A: , "Freesurfer support list" Ogg: Re: [Freesurfer] R:

[Freesurfer] mni305 volume-based analysis

Hi list, I'm configuring mkanalysis-sess to configure an analysis for FC data by FS-FAST. I do not understand how I can perform mni305 volume-based analysis. How can I configure an analysis for mni305? Specifically, which is the paradigm file in -taskreg? How is the command for group level prepr

[Freesurfer] mni305 volume-based analysis

Hi list, I'm configuring mkanalysis-sess to configure an analysis for FC data by FS-FAST. I do not understand how I can perform mni305 volume-based analysis. How can I configure an analysis for mni305? Specifically, which is the paradigm file in -taskreg? How is the command for group level prep

[Freesurfer] R: mni305 volume-based analysis

Hi list, I 'm continuing to have problem to run mni305 volume-based analysis.I have read the guide (http://freesurfer.net/fswiki/FsFastFunctionalConnectivityWalkthrough?highlight=%28mkanalysis%5C-sess%29%7C%28connectivity%29).It explains that separate mkanalysis-sess commands will need to be ru

[Freesurfer] R: Re: R: mni305 volume-based analysis

I'm sorry Doug but I should run mkanalysis-sess -mni305 for both right and left thalamus (which are taskreg). Specifically, I'm performing mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfi

[Freesurfer] error mri_glmfit-sim

Hi list, I'm performing FS-FAST for seed-based (thalamus). During mri_glmfit-sim --glmdir my-glm.wls/ --grf 1.3 neg --cwpvalthresh .0166I have this error:Input volume FOV xfm Matrix: -2.000 0.000 0.000 76.000; 0.000 0.000 2.000 -93.000; 0.000 -2.000 0.000 76.000

[Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi list, I working on the combination of MRS and FS-FAST analysis.I have extracted the grey matter within voxel (I will call it "ROI_MASK") by using FSL tools and now it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview). I'd like to import

[Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi list, I working on the combination of MRS and FS-FAST analysis.I have extracted the grey matter within voxel (I have called it "ROI_MASK") by using FSL tools and it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview).I'd like to import it

[Freesurfer] FS-FAST using a ROI as seed

Hi list,I'd like to performed FS-FAST using a ROI as seed.Should I use fcseed-config? Thus, what should I put instead of -segid?Thanks and regards. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] Constraint to FS-FAST analysis

Hi list,is it possible to put a constraint to FS-FAST analysis. More specifically use as seed a subcortical region (e.g. thalamus) and a target (e.g. frontal pole)?If yes which is the option in the command line? Stefano ___ Freesurfer mailing list Fre

[Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Thank you very much.My mask is in .nii.gz. How can I transform it in .mgz? Should I do it? Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 30-giu-2015 0.36 A: Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi

[Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi list, When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem to correspond. However, when I added the ROI_MASK.nii.gz, the orig is vanished, and is remained the ROI_MASK in correct position (and in white) and around all black. My concern is the correct binarization of ROI_MASK w

[Freesurfer] Dynamic causal modeling

Hi list, I'm performing the functional connectivity analysis by FAST.Next, I'd like to perform spectral dynamic causal model analysis (SPM, Friston et al. 2015; Crone et al. 2015) on FS-FAST output.Have you any suggestion in this matter?Thanks, Stefano __

[Freesurfer] R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi list, in the previous mail you have suggested to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in $SUBJECTS_DIR/subject/mri). I have two question please.A- my mask is on vmPFC, thus it include the both hemispheres. Should I divide it in right and left?

[Freesurfer] dwi_orig.nii.gz does not exist

Hi list, I have a strange problem with TRACULA.The analysis run fine on all subjects but on the last two, -prep command produces this error: #@# Image corrections Mon Jul 20 09:09:54 CEST 2015mri_convert $SUBJECT/data.nii.gz $SUBJECT/dmri/dwi_orig.nii.gzcp $SUBJECT/bvecs.txt $SUBJECT/dmri/dwi_or

[Freesurfer] mri_convert command line did not provide output file

Hi list,mri_convert command line did not provide output file.This error was produced during the first computations of trac-all -prep command line. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailm

[Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

My concern is whether this command line is correctfcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s SessXXX -cfg mean.ROI_MASK.configThank youStefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 20-lug-2015 19.17 A: Ogg: Re: [Frees

[Freesurfer] R: Re: mri_convert command line did not provide output file

Thanks Here is attached. INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaINFO: Diffusion root is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c $SUBJECTS/Control75/scripts/dmrirc.local -log $SUBJECTS/Control75/s

[Freesurfer] slice timing correction in preproc-sess

Hi list, preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-runproduces fmc file but fmcstc and fmcstcsm are lacking.A- The slice timing correction is performed with the command reported above? Or I should add to command line -stc (furthemore, where I should put it? S

[Freesurfer] R: Re: slice timing correction in preproc-sess

Ok.My acquisition slices interleaved.Should I add to the command line above the flag -sliceorder so odd preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder so but this is the error:3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.m

[Freesurfer] slice timing correction fmcstc files are lacking

Hi list, I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.I have acquired data using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder siemens"?The command line:preproc-sess -s Sess201 -fwhm 5 -surfa

[Freesurfer] slice timing correction fmcstc files are lacking

Hi list, I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.I have acquired data using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder siemens"?The command line:preproc-sess -s Sess201 -fwhm 5 -surf

Re: [Freesurfer] slice timing correction fmcstc files are lacking

Hi using Philips scanner (interleaved)Therefore, I'm running preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -sliceorder odd However, as you can see below stc has been not produced. file:///Applications/freesurfer/subjects/Sess101/rest/001/f.niifile:///Appli

[Freesurfer] conjunction map

Hi list, is possible to obtained a conjunction map from vlrmerge command on FS-FAST (resting state) results? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informat

[Freesurfer] ERROR: loading aseg $SUBJ/mri/MRS_MASK.nii.gz.mgz

Hi list,I'm performing FS-FAST using as seed MRS voxel (MRS_MASK). MRS_MASK shows a god overlap with orig and both of these are located in $SUBJ/mri.Firstly, I have performed:fcseed-config -segid 1 -seg MRS_MASK.nii.gz -fsd rest -mean -cfg mean.MRS_MASK.configNext,fcseed-sess -s Sess101 -cfg me

[Freesurfer] R: Re: ERROR: loading aseg $SUBJ/mri/MRS_MASK.nii.gz.mgz

Thanks. Another error is occurring:Writing to /Applications/freesurfer/subjects/Sess102/rest/001/tmp.fcseed-sess.8002/avgwf.mgh Segmentation fault after fcseed-sess -s Sess102 -cfg mean.MRS_MASK.config Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 8-set-2015 19.02 A: Ogg:

[Freesurfer] slope_age.mtx unknown

Hi list,I'm performing one group and one covariate on resting state FAST analysis.Here, I'm reporting the error.ThanksBest regards, Stefano mri_glmfit --glmdir my-glm_age.wls --y y.mgh --nii.gz --fsgd file_age.fsgd --C intercept_age.mtx —-C slope_age.mtx gdfReadHeader: reading file_age.fsgd INFO:

[Freesurfer] fast_selxavg3() failed\n

Hi list, I'm performing FS-FAST on rsfMRI.The seed is MRS voxel.I have run: 1-mri_convert MRS_MASK.nii.gz $SUBJECTS_DIR/MRS_MASK.mgz 2-fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg mean.MRS_MASK.config 3-fcseed-sess -sf sessid -cfg mean.MRS_MASK.config 4- mkanalysis-sess -ana

[Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi listi, the following error now occur: --- matlab output < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (maci64) February 11, 2014

[Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Thanks, the error occurred in the command line because I have used fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg mean.MRS_MASK.configfcseed-sess -sf sessid -cfg mean.MRS_MASK.config and the correct form is MRS_MASK without mean. fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -

[Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Yes, selxavg3-sess runs fine. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 22-set-2015 20.50 A: Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity So it is working now? On 09/22/2015 02

[Freesurfer] R: R: Re: R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

For some subject, analysis run fine.For others subjects (processes are the same for all) I have this error fcseed-sess -s Sess001 -cfg MRS_MASK.configmri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/Control01/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/subj/Sess

[Freesurfer] import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results in FSL, opening them by fslview.Could you provide me some suggestion? Thank you very much Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

[Freesurfer] import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results (conjunction maps) in FSL, opening them by fslview.Could you provide me any suggestion? Thank you very muchBest regards, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] R: import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results (conjunction maps) in FSL, opening them by fslview.Could you provide me any suggestion? Thank you very muchBest regards, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

[Freesurfer] Recon-all error after El Capitain update

Hi list, after update with El Capitain, recon-all -all produce the error reported below. Thanks srclabel = /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = SUBJECTS_DIR trglabel = ./lh.BA1.label regmethod = surface srchemi = l

[Freesurfer] R: Re: Recon-all error after El Capitain update

This is the command and the error line. Thanks. Stefano recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR # INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89;

[Freesurfer] Cortical thickness and FS-FAST on cerebellum

Hi list,I wonder whether is possible to:1) obtain cortical thickness from cerebellum and its subregions2) use cerebellum (or its subregions) as seed for FS-FAST analysis? Thanks in advance Kind regards Stefano___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] Use CA and other subfields as seed for FS-FAST

Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Piz

[Freesurfer] R: Re: Use CA and other subfields as seed for FS-FAST

Dear Eugenio,thank you very much.How can I obtain the beta version 6.0?Moreover, given that we are planning to analyze a big sample, I wonder when will be approximately released the stable's 6.0?Thanks Kind regards Stefano Messaggio originale Da: "Iglesias Gonzalez, Eugenio" Data: 3

[Freesurfer] Import FS data to FSL

Hi list, I have 2 questions, please. 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)? 2-I'd like to export cortical masks from FS to FSL. An option is mri_binarize but this way failed in probtrackx (fsl).FSL list have advised me that I should use label2surf command to

[Freesurfer] R: Re: Import FS data to FSL

Thanks Anastasia. I have some problem when I use mri_binarize.FSL list and guide advise me to use label2surf. There are a way to obtain specific labels in .label instead of .nii.gz? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: Cc: Ogg: Re:

[Freesurfer] R: Re: Import FS data to FSL

For FSL guide: Normal 0 false false false IT JA X-NONE

[Freesurfer] R: Re: R: Re: Import FS data to FSL

Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s -o -l -s,--surf input surface-o,--outoutput surface -l,--labels ascii list of label files I should provide also surface file re

[Freesurfer] R: Re: R: Re: R: Re: Import FS data to FSL

Anastasia thank you very much! I have wrote to FSL mail list. They have uploaded a new web page of FDT. Anyway, these are the commands: mris_convert lh.white lh.white.giiecho lh.BA44.label lh.BA45.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txtStefano ---

[Freesurfer] Conversion niifty to dcm

Hi list, there is a way to convert niifty or .par/.rec in DICOM? Thank you very much, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is in

[Freesurfer] Linear regression

Hi list, I have some questions, please. I performed linear regression by qdec to find the regions where the cortical thinning correlates with neuropsychological test (NPS), taking in account 3 nuisance factors. A- I individuated some posterior regions and now I'd like to build a table with part

[Freesurfer] R: Re: Linear regression

Tank you very much. A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? Finally a linear regression is done between cortical thickness of a composite region and NPS. However the authors discuss every individual region as related to disease. So a table with parti

[Freesurfer] R: Re: R: Re: Linear regression

Dear Douglas, thank you very much for you kind reply.In the paper I have 3 groups (2 diseases and 1 controls).I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically

[Freesurfer] R: Re: R: Re: R: Re: Linear regression

originale Da: charujing...@163.com Data: 5-dic-2013 2.15 A: "stdp82", "freesurfer" Ogg: Re: [Freesurfer] R: Re: R: Re: Linear regression body{FONT-SIZE:12pt; FONT-FAMILY:宋体,serif;} --> Dear Stefano, I also want to make a corre

[Freesurfer] Tracula -stat

Hi list, I'm performing -stat step but this command produces sementation fault after loading affine registration .mat. Thanks, Stefan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

[Freesurfer] hippo-subfield

Hi list, I have some question regarding hippo-subfield parcellation.If I understand the final results are thickness of each ROI but assuming a voxel of 0.5x0.5x0.5.Therefore, a correction is request. A-How is the best way to do it?B-Correction for mean thickness or ICV is advised? C-Is possible

[Freesurfer] SLFP

Hi list, SLFP is SLF III? Is there a way to obtain by TRACULA also SLF I and II, knowing the the cortical targets of the tracts? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] TRACULA -stat

Normal 0 false false false IT JA X-NONE

[Freesurfer] Yeo parcellation

Hi list, I have download the files of Yeo parcellation from ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip. I have two questions, please. A- Which is the directory where I should put these files?B-I have already run by recon-all -all all my subjects. How can I added to t

[Freesurfer] Arcuate fascicle and SLFIII

Hi list, in Wakana et al., 2007, the SLF was divided in parietal and temporal components. As I understand it, the same subdivision has been made in Yendiki et al, 2011. In details, SLFp should correspond to SLF III and SLFt to arcuate fascicle.Tractography studies showed that the anatomy of the

[Freesurfer] TRACULA statistics concern

Hi list, I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD. Which is the best way to perform statistic on TRACULA outcomes? I think that MANCOVA is too hard and it delete interesting and consolidate (in literature) results. Thanks, Stefano __

[Freesurfer] R: Re: TRACULA statistics concern

Ciao Eugenio, thank you very much for your prompt and kind response.Yes, I'm looking average over the entire support of the path distribution and their differences among 2 pathological and 1 control groups.I haven't a strong hypothesis.When I performed MANOVA, Tukey or Bonferroni post hoc find d

[Freesurfer] Thickness analysis on fetal brain

Hi list, we would like to perform cortical thickness analysis on fetal brain. We have a single shot T2 image (good quality) and T1 image (poor quality). All images are in 2D with overlapping and they are acquired by using 1.5 tesla. We have some questions: 1. Do you know a post-processing way to

[Freesurfer] ROI in FreeSurferColorLUT.txt

Hi list, I'm noting these regions in FreeSurferColorLUT.txt. How can I obtained structural information from them? 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal

[Freesurfer] R: Re: ROI in FreeSurferColorLUT.txt

Thank you very much! A last question, please. Therefore, do you are working also on SLF I and SLF II implementation in TRACULA? If yes, how much time might be required to do it? (I'm writing a paper and I may wait these new tracts). Stefano Messaggio originale Da: fis...@nmr.mgh.harv

[Freesurfer] R: labels of thalami

My apology. Here, the responce http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32645.html Messaggio originale Da: std...@virgilio.it Data: 28-apr-2014 19.11 A: Ogg: [Freesurfer] labels of thalami Hi list, I'd like to obtained .labels of thalami to use it in FSL. H

[Freesurfer] R: Re: labels of thalami

Thank you very much!! Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 28-apr-2014 19.21 A: Ogg: Re: [Freesurfer] labels of thalami Use mri_cor2label On 04/28/2014 01:11 PM, std...@virgilio.it wrote: > Hi list, > > I'd like to obtained .labels of thalami to use it in FSL. > >

[Freesurfer] labels of thalami

Hi list, I'd like to obtained .labels of thalami to use it in FSL. How can I do it? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mai

[Freesurfer] R: R: Re: labels of thalami

My apologies, but how can I visualize and check the labels obtained by mri_cor2label? Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 28-apr-2014 19.23 A: Ogg: [Freesurfer] R: Re: labels of thalami Thank you very much!! Messaggio originale Da: gr..

[Freesurfer] thalami mask (nii.gz) to import in FSL

Hi list, I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed mask in probtrackx. Thanks, Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The in

[Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

My apologies, how can I visualize mri_binarize output? I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: , "Freesurfer support lis

[Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

My apologies, how can I visualize mri_binarize output. I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: , "Freesurfer support li

[Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

[Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no. fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)data_type FLOAT32dim1 212dim2 320dim3 320dim4 1datatype 16pixdim1

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Thank you very much Michael. Now I'm running probtrackx, I will update you. Stefano Messaggio originale Da: mha...@wustl.edu Data: 29-apr-2014 22.25 A: "std...@virgilio.it", "freesurfer@nmr.mgh.harvard.edu", "Harms, Michael" Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R

[Freesurfer] FAST without preprocessing

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni

[Freesurfer] No preprocessing on FAST

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni

[Freesurfer] R: Re: R: import FS-FAST results in FSL

I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --template? It should be in Tailairach space? Where can I find the template that I should added? Thanks, Stefano subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz

[Freesurfer] R: Re: R: import FS-FAST results in FSL

Yes I would like to open with fslview (FSL) the sig.nii.gz of each subject which is computed by seed-based analysis by FS-FAST. I have mask the sig.nii.gz by fslmaths -div I have run: mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg subj/rest/001/register.dof6.dat --hemi rh --o prova

[Freesurfer] R: Re: R: Re: R: import FS-FAST results in FSL

Thank you very much, How can I export a conjunction maps from surf to volume? I need to make it to perform the DCM analysis by SPM. Stefano >Messaggio originale >Da: fis...@nmr.mgh.harvard.edu >Data: 27-ott-2015 13.21 >A: , "Freesurfer support list" >Ogg: Re: [Freesurfer] R: Re: R: imp

[Freesurfer] no voxels in mask vcsf.config

Hi list, I'm using FS-FAST. For a subject I have the error reported below after fcseed-sess -s subj -cfg vcsf.config.The segmentation of the structural image is fine. $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects/fMRI cmdline mri_glmfit --y /

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