[Freesurfer] A question about the Freesurfer version compatibility of Tracula

Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of an earlier version of FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the subjects in the data set with 5.1.0. Would running Tracula on 5.0.

[Freesurfer] Creation of normalized cortical regions of interest

Hi,freesurfers: Recently,I read a paper which used freesurfer to processed their data,this is the paper's link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159 In this paper,the antor said : "One of the critical steps of the whole procedure was to partition the

[Freesurfer] question about qdec

Hi all: I have three groups of subjects (major depression disorder,slight depression disorder and contrast),i want to use qdec to obtain the statistical significant areas containing difference of cortical thickness measurment among them. But there are some errors appearing when i run the gr

Re: [Freesurfer] more on fieldsign problems-

are you sure it's registered well to the anatomical/surface? On Thu, 7 Jul 2011, Michelle Umali wrote: > Hi Doug, > The eccen and polar maps look ok, although activation tends to be > limited to the occipital poles and lateral surface not really along > the calcarine. > > Is it possible to find o

[Freesurfer] QC Montages error

I am getting an error when using a script that combines these 3 actions: preproc.sh std_map_qc_montages.bash put_tpef.bash Freesurfer version 4 SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects Script: /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh It looks like

Re: [Freesurfer] more on fieldsign problems-

Hi Doug, The eccen and polar maps look ok, although activation tends to be limited to the occipital poles and lateral surface not really along the calcarine. Is it possible to find out how the colors in the eccen and polar images correspond to positions in the stimulus using rtview? There's

[Freesurfer] preprocessing qc

Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] Error with Tksurfer

Hi Antonella, did bert inflated look ok on the other computer? Usually this problem goes away if you update the video card driver. cheers Bruce On Thu, 7 Jul 2011, Antonella Kis wrote: Good afternoon Bruce, I am still trying to fix my error related to the surface image display when using

Re: [Freesurfer] talaraich ERROR

Yep, use tkregister2 --s subject --fstal there are instructions in the trouble shooting tutorial on the wiki. doug Carolina Valencia wrote: > Hi FSexperts, > > I have a case of a child with /Hydrocephalus and cortical dysplasia, > the patient has a subcutaneous ventriculo-peritoneal shunt that

Re: [Freesurfer] Matlab and FS {Disarmed}

Hi Carolina   You simply need to add the path  ‘your FS installation dir/freesurfer/matlab’ to the search path in Octave:   addpath(‘your FS installation dir/freesurfer/matlab’);   For example, to build a histogram of cortical thickness values for the first subject of your study,  you can try:  

[Freesurfer] talaraich ERROR

Hi FSexperts, I have a case of a child with *Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR* # #@# Talairach Failu

Re: [Freesurfer] Retinotopy stimuli

Hi Anders, I agree with the points Jon made. 8 Hz flicker is also what I use. I haven't tried lower frequencies, but I think you would definitely have reduced SNR if you did. I also use rather thin wedges and rings and smoothly vary their position. I would add that a longer cycle duration

Re: [Freesurfer] Retinotopy stimuli

hi anders, the optimal set of stimulus parameters will depend somewhat on what cortical area(s) you are trying to map and on the details of your acquisition. in general, stimulating with both clockwise- and counterclockwise-rotating wedges for polar angle mapping and with both expanding and contr

Re: [Freesurfer] tracula bvecs problem

Great, good to know. My LANG is en_US.UTF-8, everything else is not set. On Thu, 7 Jul 2011, Franz Liem wrote: > Dear Anastasia & all. > > I fixed it. > > The problem was my LOCALE setting which leads to different handling of > decimal separators by awk (for further details see > http://object

Re: [Freesurfer] DOF and smoothing in mri_glmfit

The problem with doing the smoothing at the first level in FEAT is that it will be volume-based, not surface-based. I'm not sure what to tell you about using the varcopes. They will certainly be very noisy without smoothing, so probably smoothing is a good idea, even if it's volume-based. doug

Re: [Freesurfer] Retinotopy stimuli

I'd also be very interested to hear about good reinotopic stimuli; we've used 6Hz and 14 ring sizes for eccentricity mapping in the past. Thomas Ballinger On Thu, Jul 7, 2011 at 3:56 AM, Anders Hougaard wrote: > Dear freesurfers, > > > Which stimuli do you think provide the best retinotopic maps

Re: [Freesurfer] DOF and smoothing in mri_glmfit

Dear Doug, Thank you so much. I completely see you point, but I have re-run the 1st level feat without smoothing just because it has been recommended not to smooth in the volume and then transfer it onto the surface, but rather first smooth on the surface (http://surfer.nmr.mgh.harvard.edu/fswiki/

Re: [Freesurfer] DOF and smoothing in mri_glmfit

Hi Aga, your commands look right. For the DOF, it should be the sum of the DOFs from all the runs (probably won't make much of a difference). Smoothing is a bit of an issue when you want to look at individual results. Technically, you should smooth before you do the first level analysis (ie, be

[Freesurfer] DOF and smoothing in mri_glmfit

Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECT

Re: [Freesurfer] QDEC table

the 'generate stats data tables' button in the Subjects tab will do this. see the section 'Stats Data Import' in the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis which is copied here: > It is possible to import the aseg and aparc data from the > FreeSurfer-pro

Re: [Freesurfer] more on fieldsign problems-

Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug Michelle Umali wrote: > Dear all, > I've been having issues with my fieldsign images all I g

Re: [Freesurfer] make_average_subject error

Hi Leo, check to see if that subject's analysis is up-to-date. This usually happens when it was only partially re-run. doug leonardo kay wrote: > Hi all > > Could anyone help me with this error: > > MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 > i=5A595959, in_array_size=13

Re: [Freesurfer] Viewing a multi-frame image?

Dear Doug, Yes, it works, thank you so much! Cheers, Aga On 7/7/11 3:57 PM, "Douglas N Greve" wrote: > Hi Aga, try View->Configure->Overlay. The config window will have a time > point entry at the top. > doug > > Agnieszka Burzynska wrote: >> Dear all, >> I created a 3-frame image using a comma

[Freesurfer] make_average_subject error

Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says

Re: [Freesurfer] Viewing a multi-frame image?

Hi Aga, try View->Configure->Overlay. The config window will have a time point entry at the top. doug Agnieszka Burzynska wrote: > Dear all, > I created a 3-frame image using a command similar to: > mris_preproc --target fsaverage --hemi lh --fwhm 5 \ > --out xrun/lh.cope1.mgh \ > --iv fbert1

[Freesurfer] Viewing a multi-frame image?

Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer

Re: [Freesurfer] matlab loading problem (mkcontrast, selxavg3-sess)

Hi Paola, I can't tell from the output what went wrong. One thing that may be going wrong is that you might not have the matlab binary in your path. From a terminal, type 'which matlab' (no quotes). Also, please don't send logs and error messages in rtf or doc formats -- it makes it harder for

Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?

The conversion from PET to MNI305 uses two registration steps. One from PET to anatomical, one from anat to mni305. bbregister handles the first one, so 6 dof is fine. doug Joao Pereira wrote: > Dear Freesurfers, > > I was wondering if you could help me clarify one question I have re > the reco

Re: [Freesurfer] cortical dysplasia

Carolina, We have worked with several cases of MCD (including cortical dysplasia). We have published this paper: https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf It may help. But in most cases of cortical dysplasia (not Gray matter heterotopia cases) you'll find a ticker cortex not

[Freesurfer] cortical dysplasia

Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the

Re: [Freesurfer] Matlab and FS

Hi Jorge, Thanks for your reply, I installed Octave in the Ubuntu machine, Should I setup something in order to use the FS commands? Best regards, Carolina 2011/7/5 jorge luis > > > Hi Carolina > > ** > > There is a directory freesurfer/matlab which contains several matlab-based > scripts

[Freesurfer] freeview load fiducials from 3DSlicer

Hi guys, I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to import them within freeview? Those points look like label,x,y,z,[flag],[flag] i.e. P,57.799,-49.1799,13.07,1,1 P,-4.05607,-47.1519,8.93645,1,1 thank in advance. g. ___ F

[Freesurfer] QDEC table

Hi freesurfers Do anyone know if it's possible to automatically enter in the QDEC table the gray matter volume of every subject in the study, to avoid entering this item manually for each one ? Best regards. -- Ignacio. ___ Freesurfer mailing list Fre

Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?

Hi Joao You are registering to that subject's anatomicals, not a template, so 6 should be enough Cheers Bruce On Jul 7, 2011, at 6:43 AM, Joao Pereira wrote: > Joao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

[Freesurfer] bbregister - Are 6 dof enough for MNI305?

Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used wi

Re: [Freesurfer] tracula bvecs problem

Dear Anastasia & all. I fixed it. The problem was my LOCALE setting which leads to different handling of decimal separators by awk (for further details see http://objectmix.com/awk/716715-awk-different-decimal-separator-different-linux-distros.html). My original setting was: % locale LANG="de_

Re: [Freesurfer] Error while loading qdec project file

Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this be

[Freesurfer] Retinotopy stimuli

Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR =