[Freesurfer] Cortical Segmentation reliability in Mid-Line structures

Dear All, I wonder if you have experienced or there is any report on cortical segmentation reliability in the mid-line structures of the brain, so one should take them into consideration in running group differences with Qdec? Best regards, Amirhossein Manzouri

Re: [Freesurfer] Cortical Segmentation reliability in Mid-Line structures

Hi Amirhossein which structures do you mean? Like the ventricles? We usually mask those regions out using the ?h.cortex.label. The surfaces should be "frozen" in those regions in any case, meaning that the white and pial are in the same location (and the thickness is 0) cheers Bruce On Mo

[Freesurfer] dt_recon error

Hi All, I ran dt_recon and got the following error. Can someone suggest how to fix this ? I have attached the dwi-infodump.dat file for more information. Thanks a lot for the help. Best Rito #@#--- Fitting Tensors Mon Aug 11 07:29:29 EDT 2014 cd /Users/iron/rito/V

[Freesurfer] Any good cortical segmentation methods for brains with infarct or tumors?

Hi, Does anyone have recommendations for good automated cortical segmentation tools for brains with infarct (so some brain missing) or tumors? I am under the impression that FreeSurfer is not reliable in these cases. If I am incorrect, any pointers on how to use FreeSurfer in these cases would be

Re: [Freesurfer] lobes gyrification

hi thank you marie. Ive tried this but it doesnt give me one single spreadsheet for the value of each subjects lgi, just produces a file in each subjects stats directory. How do I make a spreadsheet with everybody's lgi values in it? Kind Wishes, Melly From: marie.sch...@unige.ch To: freesurf

Re: [Freesurfer] lobes gyrification

Hi Melly, You can use aparcstats2table from the file you created: aparcstats2table --subjects …. --hemi lh --meas thickness --parc aparc_lgi --t summary_lgi.txt Here you'll read the column "thickness" in the lh.aparc_lgi.stats file that you have created with mri_anatomical_stats (i.e. corr

[Freesurfer] midline cortical thickness

Question regarding reliability of midline cortical regions by Amir - it refers to the cingulate cortex, the cuneus, precuneus. Sincerely Ivanka Savic M.D., PhD > Professor of Neurology > Karolinska Institute > Dept of Women’s and Children’s Health > and Neurology Clinic,Karolinska Hospital, Q2:07

Re: [Freesurfer] dt_recon error

Hi Rito. It is not finding information about the gradient table that was used for the acquisition. If you have that information you can use the below option to manually include it --b bvals bvecs If you do not you could try using load_dicom in order to grab that information. Lilla On Mon,

[Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

Just wanted to pose this question again to the Freesurfer community: Can anyone provide any advice on how to justify using the V1, V2 labels in FreeSurfer in clinical populations without also collecting functional retinotopy data? Thanks! Krista -- Forwarded message -- From: kris

Re: [Freesurfer] mri_em_register intervention?

It looks more likely that it is a problem with the skull stripping. If you clone the brain voxels back in and rerun do things work? > On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna" > wrote: > > I am having trouble getting a usable brainmask for one of my subjects - > a screenshot of the

Re: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

Hi Krista, Please refer to the following publications from Geoff Aguirre's lab - http://www.ncbi.nlm.nih.gov/pubmed/23041195 http://www.ncbi.nlm.nih.gov/pubmed/24676149 All templates are in fsaverage_sym space in .mgh format and are available for download https://cfn.upenn.edu/aguirre/wiki/pu

Re: [Freesurfer] error loading subjects in QDEC

Katie, Hi, is the SUBJECTS_DIR set to the proper directory? I see from the output that it is set to: SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' which seems to imply that it might be set to the location of your freesurfer installation, and not t

Re: [Freesurfer] error loading subjects in QDEC

Hi Nick, Thanks for responding. We found a solution to the issue with the SUBJECTS_DIR (which was pointing to the location of our data, not the FS installation). This issue appeared after doing some software updates on our cluster (including Ubuntu). Here is how we fixed it: sudo mv /bin/sh

Re: [Freesurfer] FsFast Functional Connectivity Analysis

There's nothing even when the threshold is set to 0. I just checked the preprocessing outputs. I can see normal-looking volumes fmcpr.nii.gz fmcpr.up.nii.gz fmcpr.up.sm6.mni305.2mm.nii.gz But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or fmcpr.up.sm6.fsaverage.rh.nii.gz On

Re: [Freesurfer] FsFast Functional Connectivity Analysis

did you check the registration? On 08/11/2014 03:53 PM, Jiahe Zhang wrote: > There's nothing even when the threshold is set to 0. > > I just checked the preprocessing outputs. I can see normal-looking > volumes > fmcpr.nii.gz > fmcpr.up.nii.gz > fmcpr.up.sm6.mni305.2mm.nii.gz > > But there is not

Re: [Freesurfer] FsFast Functional Connectivity Analysis

I'm not sure how to check the registration. I see a register.dof6.dat being produced for each run but I can't tell if it contains the correct parameters. How can I tell if the registration was accurate? On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve wrote: > did you check the registration? >

Re: [Freesurfer] FsFast Functional Connectivity Analysis

two ways: 1. run tkregister-sess to visually check them 2. look at the first value in register.dof6.dat.mincost. It is hard to say what a threshold is for a good registration, but typical values are about .5 or so. If it is .8 or more, it is probably a problem (and probably the initialization i

Re: [Freesurfer] FsFast Functional Connectivity Analysis

Both looked fine. First value in .mincost is .45 On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve wrote: > two ways: > > 1. run tkregister-sess to visually check them > 2. look at the first value in register.dof6.dat.mincost. It is hard to > say what a threshold is for a good registration, but

Re: [Freesurfer] FsFast Functional Connectivity Analysis

How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do this, try it tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t fmcpr.up.sm6.fsaverage.lh.nii.gz This will bring up an overlay as well as a time course On 08/11/2014 05:05 PM, Jiahe Zhang wrote: > Both

Re: [Freesurfer] error loading subjects in QDEC

Hi Nick, We solved this. Thanks for your help, Kate From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [katie.mclaugh...@childrens.harvard.edu] Sent: Monday, August 11, 2014 3:42 PM To: Fr

[Freesurfer] Mac OS X update

Hi all,   I have a simple doubt: I am updating my MAC OS X from Snow Leopard to Mavericks.   I am worried if FreeSurfer is going to run perfectly in the new OS X?   Thank you,  Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

Re: [Freesurfer] -hippo-subfields

Hi, Greg I use to process my subjects with: recon-all -s subjid -all -hippo-subfields The -all flag makes the program run all the 3 stages (autorecon1, autorecon2 and autorecon3) in sequence. Only after this it starts the hippo-subfields stage. If you do not have any special reason to run each au

[Freesurfer] fsaverage cortex thickness

Hi, all, How to calculate the mean cortex thickness of fsaverage? Thanks! Wilder___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

[Freesurfer] Flipped Hemisphere longitudinal analysis

Dear Freesurfers, Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres? I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain. What I am planning: flip all he