[Freesurfer] hematoma problem

hi I am working on severe TBI and most of them suffer from large hematoma and according to litterarture, the apearance on T1 changes accordind to the stage of the trauma, from 3days (early suba acute) to 14 days (late subacute) the T1 signal from hematoma is Hyperintense and after that it becom

[Freesurfer] rs-fMRI data on pial surface

Hi Freesurfers, For this analysis I plan to do, I want to map resting-state data in native (T1) space to the pial surface. The command I use for this is: mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh So the intention is to ave

Re: [Freesurfer] hematoma problem

sorry, I don't have any experience with hematomas. You'll just have to try it and see On Tue, 14 May 2013, LAOUCHEDI MAKHLOUF wrote: > > hi > > > I am working on severe TBI and most of them suffer from large hematoma and > according to > litterarture, the apearance on T1 changes accordind to

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: >> >> >> >> >> >> >> sxa3pwd = /home/...removed... >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 >>

Re: [Freesurfer] Show curvature and show overlay

Dear freesurfer experts, I am new to freesurfer and I want to project my single-subject MVPA (obtained in Matlab) results on a single-subject brain surface with curvature. I followed the steps from the tutorial: - reconstructed individual subject's brain surface - wrote my MVPA results map as a

Re: [Freesurfer] Show curvature and show overlay

Hi Irina you need to load the overlay (file->load overlay or -overlay on the cmdline) and the curvature file (file->load curvature or just -sulc on the cmdline I think) cheers Bruce On Tue, 14 May 2013, Irina Simanova wrote: > Dear freesurfer experts, > > I am new to freesurfer and I want to

Re: [Freesurfer] Still confused by group analysis..

Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis.. On 12 May 2013 16:45, Tudor Popescu wrote: > Dear Freesurfer experts, > > I very much appreciate your help with an additional set of questions.

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Soo-Eun Chang souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Soo-Eun Chang http://www.linkedin.com/e/-qq80um

Re: [Freesurfer] rs-fMRI data on pial surface

Hi Rene, do you want it on the pial surface or the average over the ribbon? If the pial surface, then use your cmd below but use --projfrac 0. If you want the average use your cmd below but change pial to white (or don't spec --surf) doug On 05/14/2013 08:00 AM, René Besseling wrote: > Hi Free

Re: [Freesurfer] Still confused by group analysis..

On 05/14/2013 10:05 AM, Tudor Popescu wrote: > Not sure whether anyone'd seen my last email (below). Again apologies > for the multitude of questions, I hope this is the last batch for this > analysis.. > > On 12 May 2013 16:45, Tudor Popescu > wrote: > > Dear Frees

Re: [Freesurfer] Still confused by group analysis..

Dear Doug and others, I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you r

Re: [Freesurfer] Still confused by group analysis..

Hi Arman, I have not followed the FSL thread, but you would only do this if you have a column of ones in your design matrix. Itdoes not imply that gender is being treated as a continous variable. A continuous variable for gender means that male=1 and female=2. This implies that you expect femal

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

Joerg, I'm guessing you have some matlab setup script that has run prior to the freesurfer setup. I see this output: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 which is not something freesurfer would link against or require. normally it should use /usr/lib64/libstdc++.so.6. try runn

Re: [Freesurfer] Still confused by group analysis..

> > > 1) In a design with group and gender as discrete factors and age > > as a continuous factor, why is it that QDEC only displays the > > contrast "Does the avg thickness, accounting for gender, differ > > between group1 and group2?" and not also "..acounting for gender > > a

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

Hi, all I have just finnished my FS 5.3-Beta recon-all test in Fedora 18 and compared to FS 5.2 in CentOS6. Both OS are installed in the same machine but different HDs. I used recon-all -all -hippo-subfield in the same subject for both runs and it worked great. The time in both versions were simil

[Freesurfer] Problems with hippocampus subfields segmentation

Hi FreeSurfer Experts! I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields: recon-all -s my_subjects -hippo-subfields The shell output is

[Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface

Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you S

[Freesurfer] Recon-all error

Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia -- SUBJECT MGH009_SurferOutput DATE Mon May 13 11:25:37 EDT 2013 USER miaborz HOST huygens PROCESSOR x86_64 OS Linux Linux hu

Re: [Freesurfer] Problems with hippocampus subfields segmentation

Hello Luke, A patch was released to fix this problem. In order to fix this issue please follow these instruction: 1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/kvl.zip 2) Overwrite the existing kvl files in your /Application/fr

[Freesurfer] problem with func2roi-sess

Hello Freesurfers, I would appreciate any advice or help you can provide. I am using the following command, run under Stable 3 (to keep the current analysis comparable to prior papers): func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_s

Re: [Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface

Just run the next step, ie, mris_preproc but leave off the --paired-diff. Then run mri_concat preproc.out.mgh --mean preproc.out.mean.mgh doug On 05/14/2013 04:12 PM, Subhabrata Chaudhury wrote: > Hi, > I want to create an average thickness map of lh and rh. I have run > surfreg steps to map lh

Re: [Freesurfer] problem with func2roi-sess

it looks like ther is something wrong with that label On 05/14/2013 04:34 PM, jwa...@nmr.mgh.harvard.edu wrote: > Hello Freesurfers, I would appreciate any advice or help you can provide. > > I am using the following command, run under Stable 3 (to keep the current > analysis comparable to prior pa

Re: [Freesurfer] Recon-all error

Hi Mia, I think you meant to attach the recon-all.log instead of the recon-all.error, the former is more informative. Regardless it looks like the talairach registration step failed for this subject. See this wiki page for info on checking and fixing that if necessary. https://surfer.nmr.mgh.

Re: [Freesurfer] Recon-all error

sorry, recon-all.log attached! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, May 14, 2013 4:23 PM To: freesurfer Subject: [Freesurfer] Recon-all error Hi freesurfers, I recently

Re: [Freesurfer] Recon-all error

Mia, Hi, in looking at the mri/orig/001.mgz, the image in the sagital and coronal planes look inverted. also, i noticed this mri_info: dimensions: 566 x 256 x 992 voxel sizes: 1., 1., 1. which seems like unusual input. how was this converted from the dicom? did it necessitate

Re: [Freesurfer] problem with func2roi-sess

I have checked the label file directly - it is of comparable size with others, and has the same structure. I've rerun the mri_cor2label command and regenerated the labels for all subjects. Most confusing, func2roi works for some subjects in this cohort and not others. In contrast, the whole coho

[Freesurfer] 5.3 mri_convert bug?

Hi, Tried running recon-all on two different linux systems and same error occurs in the mri_nu_correct.mni.log when running mri_convert on the nu1.mnc ie.. . . . Processing:.Done Processing:..