Re: [Freesurfer] mean gyrification index

External Email - Use Caution Yes, I did replace question marks with left and right. Thank you so much, Douglas. With regards Vittal On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve wrote: > Are you using actual question marks or are you replacing them with l or r? > (you

[Freesurfer] vol2surf: lesion overlap across group into surfaces

Dear FS Experts, I would like to show the distribution and overlap of lesions on an average inflated brain surface as a heat map. I have a 150 subjects of which I’ve made masks of T2 lesions and moved into their respective subject-T1w-spaces (using T1.mgz as reference) where I have

Re: [Freesurfer] mean gyrification index

External Email - Use Caution Try this for the left hem. This command includes the excludeid = 0 mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/subject_ID/label/lh.cortex.label --i $SUBJECTS_DIR/subject_ID/surf/lh.pial_lgi --excludeid 0 --sum lh.aparc.pial_lgi_lh.stats

[Freesurfer] longitudinal MRI and DTI registration

External Email - Use Caution Hi, I was conducting a longitudinal DTI analysis. However, MRI and DTI brain scans were scheduled at different time frames. Should I be concerned that for example MRI was taken at 9/1/2006 and nearby DTI was taken on 10/1/2007 or 10/1/2009, which may

Re: [Freesurfer] Make BEM with corrected brainmask

I'm not sure, but you might be able to just create a surface from the brain mask with mri_binarize --i brainmask.mgz --min 0.5 --surf brainmask.surf You can smooth it a bit if you add --surf-smooth 2 where 2 is the number of iterations (more for smoother) Try that On 9/9/2020 6:01 PM, Kadwani,

Re: [Freesurfer] mri_volsynth question

Load $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz into freeview and find the voxel where you want it to be centered. Then run mri_volsynth as you have below but add --delta-crsf C R S 0 where C, R, S are the col, row, slice from the voxel you found in freeview On 9/9/2020 5:39 PM, Nasiriavanaki,

[Freesurfer] Make BEM with corrected brainmask

Hi, Why does the "mri_watershed" function create a new brainmask? Is there a way to create BEM surfaces from an existing or already corrected brainmask? I had manually edited the brainmask during recon-all process. After the recon-all process completed, the pial surfaces looked good. But when

[Freesurfer] mri_volsynth question

Hi I am trying to make a subcortical 5 mm sphere ROI around a talairach coordinate. I am using the below command, but when I visualize it, it doesn’t look at the correct location. I see the same question in forum (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html), I

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

See attached spreadsheet! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Wednesday, September 9, 2020 at 11:19 To: "freesurfer@nmr.mgh.harvard.edu"

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

please send the full command line and terminal output On 9/9/2020 3:19 PM, Meaghan Perdue wrote: External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only

Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

0.09940 and 0.10338 seem pretty close to me:). The summary file has Hi and Low which is the 95% confidence interval assuming a binomial model at the mean prob On 9/9/2020 3:24 PM, freesurferl...@gmx.com wrote: > External Email - Use Caution > > Thanks, I was looking for the higher

[Freesurfer] I

External Email - Use Caution In Get Outlook for iOyiS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mean gyrification index

Are you using actual question marks or are you replacing them with l or r? (you have to replace) On 9/9/2020 2:26 PM, vittal korann wrote: External Email - Use Caution I did that, but the error remains the same. mri_segstats --slabel CSRI001 ?h  

[Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only occurs when we try to run the permutation on the LH for thickness. We've been able to run the

Re: [Freesurfer] mean gyrification index

External Email - Use Caution I did that, but the error remains the same. > mri_segstats --slabel CSRI001 ?h $SUBJECTS_DIR/CSRI001/label/?h.cortex > --i $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum > h.aparc.pial_lgi-csri001.stats On Wed, Sep 9, 2020 at 11:32 PM Douglas N.

Re: [Freesurfer] mean gyrification index

You need to include the hemisphere in the --slabel arguments (maybe the 2nd one) On 9/9/2020 2:10 PM, vittal korann wrote: External Email - Use Caution Dear Douglas Thank you for your help! I got an error while executing the mris_segstats command. Command: mri_segstats

Re: [Freesurfer] mean gyrification index

External Email - Use Caution Dear Douglas Thank you for your help! I got an error while executing the mris_segstats command. Command: > mri_segstats --slabel CSRI001?h > $SUBJECTS_DIR/CSRI001/label/?h.cortex.label --i > $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum

Re: [Freesurfer] mean gyrification index

External Email - Use Caution This command includes the excludeid = 0 mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/subject_ID/label/lh.cortex.label --i $SUBJECTS_DIR/subject_ID/surf/lh.pial_lgi --excludeid 0 --sum lh.aparc.pial_lgi_lh.stats From:

Re: [Freesurfer] mean gyrification index

I think that should work On 9/9/2020 12:59 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution I have used this for mean GI per hemisphere: mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum Jim

Re: [Freesurfer] mean gyrification index

External Email - Use Caution I have used this for mean GI per hemisphere: mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve

Re: [Freesurfer] mean gyrification index

You can use mri_segstats with the --slabel option, specifying the ?h.cortex.label and using the gyrification as input On 9/9/2020 12:54 PM, vittal korann wrote: External Email - Use Caution Thank you so much, Douglas. Could you please guide me to obtain the global mean gyrification

[Freesurfer] mean gyrification index

External Email - Use Caution Thank you so much, Douglas. Could you please guide me to obtain the global mean gyrification index for each subject? With regards korann ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Extending the pial surface

Hi Monica We need a bit more detail to figure out why things are going wrong. Can you send screenshots or upload a subject? Is the white matter in that region already 110? Sometimes adding control points in the subjacent wm will bring intensities up enough to correct the pial. You can also

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

External Email - Use Caution Ok. So you prefer -hires since surface placement at hi res is similar to conf2hires? Get Outlook for Android From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve

Re: [Freesurfer] Mean Gyrification index

It is giving you values for two segmentations: inside the label and outside the label. Use --id 1 to get only values inside the cortex label On 9/9/2020 11:27 AM, vittal korann wrote: External Email - Use Caution Dear FreeSurfer experts I am working on the gyrification index of

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:    

Re: [Freesurfer] Freesurfer Licensing

no permission is needed. you will need to include the license text somewhere in your product distribution though. On 9/8/2020 2:54 PM, Rollo, Patrick wrote: External Email - Use Caution Hi all, My group is working on a software platform with the hopes of some level of

Re: [Freesurfer] Mean Gyrification index

External Email - Use Caution Dear FreeSurfer experts I am working on the gyrification index of schizophrenia patients. I had collated global brain values such as thickness, GM, and WM volumes. In addition, I wanted to tabulate gyrification values. Using the below link I was able

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

Yea, I would not say it is the best way to do QC. But just correlating the volumes themselves should be meaningful On 9/9/2020 10:29 AM, Chris Vriend wrote: External Email - Use Caution Dear Eugenio, I tested it on 103 subjects. The asymmetry index is significantly different

Re: [Freesurfer] Extending the pial surface

Can you send a pic? On 9/9/2020 10:57 AM, Monica Bondy wrote: External Email - Use Caution Hi Freesurfer Developers, I was hoping to get some advice on fixing pial surface error so we can calculate cortical thickness. In several patients, although the aseg is fine, the red outline

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

External Email - Use Caution Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)? Get Outlook for Android From:

[Freesurfer] Extending the pial surface

External Email - Use Caution Hi Freesurfer Developers, I was hoping to get some advice on fixing pial surface error so we can calculate cortical thickness. In several patients, although the aseg is fine, the red outline for the pial surface is missing parts of the cortex (not the

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Falk and Doug, thx for clarifying. 

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

External Email - Use Caution Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness,

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

External Email - Use Caution Dear Eugenio, I tested it on 103 subjects. The asymmetry index is significantly different from 0 (symmetric) for both aseg and ThalamicNuclei.v12. Also when you compare the asymmetry index across segmentation methods (either using paired or

Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

Can you try using mri_convert? Like, mri_convert mni152.nii.gz --apply_inverse_transform xform.m3z subject.mgz Let me know if that works On 9/8/2020 8:28 PM, Noriana Jakopin wrote: External Email - Use Caution Hello, I just wanted to follow up on this and see if anyone had any

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

On 9/9/2020 9:07 AM, Park, James wrote: External Email - Use Caution Dear Freesurfer Team, Thank you for this update. How can I replace the current recon-all script with this new script? Do I just replace the recon-all script located in the “bin” folder with this new script?

Re: [Freesurfer] runmrispreproc.sh, error

you'll have to give us ore info than that https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 9/9/2020 6:56 AM, Francesco Macchione wrote: External Email - Use Caution we contact you for some problems in the group analysis using MrisPreproc script  (freeSurfer). We followed all

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will

Re: [Freesurfer] Log transformation vertex-wise

External Email - Use Caution Yes, that worked. Thank you. Douglas N. Greve schrieb am Di., 8. Sep. 2020, 17:04: > you just want to compute the log of the voxel values in a volume? You can > use fscalc > > On 9/8/2020 6:30 AM, Jose Graterol wrote: > > External Email -

Re: [Freesurfer] recon-all exited with errors

External Email - Use Caution Thanks Douglas. I downloaded and installed the latest version 7.1.1 and recon-all with no errors. On Tue., Sep. 1, 2020, 10:21 a.m. Douglas Greve, wrote: > Try looking at our wiki > >

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

External Email - Use Caution Dear Freesurfer Team, Thank you for this update. How can I replace the current recon-all script with this new script? Do I just replace the recon-all script located in the “bin” folder with this new script? Additionally, I was wondering if you knew

[Freesurfer] runmrispreproc.sh, error

External Email - Use Caution we contact you for some problems in the group analysis using MrisPreproc script (freeSurfer). We followed all the instructions provided in the Andy's Brain Book, Tutorial 8. We first downloaded the shell script runmrisPreproc.sh, but when we try to

Re: [Freesurfer] Permission denied mri_surf2surf

External Email - Use Caution Hello Ellen, I suspect that you really do not have the system privileges to read/write every subject directory. I have run into this with other commands that scan multiple subject directories. Assuming there is one top level directory that contains

[Freesurfer] Permission denied mri_surf2surf

External Email - Use Caution Dear experts, I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

External Email - Use Caution Hi Jim, The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to