[Freesurfer] reusing mri_surf2surf transformation

Hi, I need to convert a big number of scalar surface maps from fsaverage to one particular subject space. This means running mri_surf2surf command many times. For each execution the same transformation is calculated and then applied. Since estimating the transformation take a substantial amount of

Re: [Freesurfer] aparcstats2table

Hi Dr. Greve, Please find the attached qdec file, along with diagnosis file which I used in QDEC, and this is the same qdec file I trying to use for the aparcstats2table command. Thanks. PS: I was also wondering (a) how can I average thickness stats (b) are these in fsaverage (standard) space an

Re: [Freesurfer] AAL atlas

We don't support the AAL atlas. The AAL atlas is just an atlas mapped through the volume transform into the individual subject's space. It does not take into account any landmarks and will be only approximate at best. If that is what you really want to do, I would suggest posting to the list of

[Freesurfer] AAL atlas

Hi all! I'm very new using FS and I have some questions. I have been doing parcellations with the FreeSurferLUT on a few subjects, with the comand recon-all and it worked OK. Now I'd want to try with the AAL atlas, I mean, I want my subject's brain parcellated in the AAL atlas. I have the template

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

You can just mri_segstats --i thickness.stack.mgh --seg cache.th30.pos.sig.ocn.nii.gz --excludeid 0 --avgwf thickness.stack.cluster.dat Each row in thickness.stack.cluster.dat will be a subject, and each column is a cluster On 11/09/2016 04:16 PM, Elijah Mak wrote: > Hi Freesurfer Team, > >

[Freesurfer] Extracting structural measures from trend-level PET clusters

Hi Freesurfer Team, 1) We've found some subtle differences in tau accumulation between two groups. Unfortunately, it does not survive mri_glmfit-sim (voxel threshold 0.001, cwp < 0.05). Still, I would like to extract the structural measures from the uncorrected tau clusters (p<0.001). What is the

Re: [Freesurfer] Assessing local correlations across 2 modalities

That looks correct to me. doug On 11/09/2016 04:07 PM, Elijah Mak wrote: > Hello, > > Thanks Doug for your help on this previously. I am quite puzzled by > the vertex-wise local correlations that I've found (i.e more tau > thicker cortex)... and before I go down the rabbit hole of trying to

Re: [Freesurfer] Assessing local correlations across 2 modalities

Hello, Thanks Doug for your help on this previously. I am quite puzzled by the vertex-wise local correlations that I've found (i.e more tau thicker cortex)... and before I go down the rabbit hole of trying to dissect what could be happening, I'd like to check if one of the steps in my workflow ha

Re: [Freesurfer] mri_convert slope scale

I think we actually apply the scaling, so including it in the output would be inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote: > Hello, > > We have been using mri_convert to convert our dicoms into .nii niftis. > There is an entry in the .nii header for the slope scale, but > mri

Re: [Freesurfer] GM = SurfArea x Thick

It should be relatively close, but they will not be identical since the volume calculation is not linear On 11/09/2016 03:40 PM, Daya P wrote: > Hi all, > > I grey matter volume supposed to be equal to surface area x average > thickness in each ROI when looking at mris_anatomical_stats for > i

Re: [Freesurfer] GM ROI list?

OK, then, I think that sorts out all my questions on this issue at this time. Thanks for the discussion and suggestions. --pt On Wed, Nov 9, 2016 at 3:34 PM, Douglas N Greve wrote: > That looks like a good list, but we don't keep track of all these > things. To add to it, we have wmparc.mgz w

[Freesurfer] GM = SurfArea x Thick

Hi all, I grey matter volume supposed to be equal to surface area x average thickness in each ROI when looking at mris_anatomical_stats for individual subjects? Thank you, Daiana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] GM ROI list?

That looks like a good list, but we don't keep track of all these things. To add to it, we have wmparc.mgz which is segmented WM (3000-3035, 4000-4035). On 11/09/2016 03:00 PM, P Taylor wrote: > The FreeSurferColorLUT.txt file has over 1,200 regions listed in it, > but I assume that not all of

Re: [Freesurfer] latest version of mri_glmfit-sim?

We are recommending that you not attempt to use qdec for multiple comparisons correction. Please use mri_glmfit-sim from the command line on the output folder created by qdec On 11/09/2016 01:39 PM, Elijah Mak wrote: > H >

Re: [Freesurfer] mri_convert scaling

Can you send the terminal output from when you run mri_convert? On 11/09/2016 11:24 AM, Funk, Quentin wrote: > > All, > > I have some DICOM files from a pet scan and an MRI. I viewed the files > in three different ways: > > > 1. Opened the DICOM's directly in a viewer (Pmod) > 2. Used mri_conv

Re: [Freesurfer] 1st level fMRI analysis maps looking strange

That is pretty weird. I would first check the fMRI-FS registration (though I doubt this is the problem). I would then look at the brainmasks. There are several in each fmri run under the masks folder. I would check brain.nii.gz first (using freeview or tkmedit -- does the mask look good? Or doe

[Freesurfer] mri_convert slope scale

Hello, We have been using mri_convert to convert our dicoms into .nii niftis. There is an entry in the .nii header for the slope scale, but mri_convert appears to discard this value instead of copying it into the header (whereas mricron retains this value) We prefer to use mri_convert. Is ther

Re: [Freesurfer] GM ROI list?

The FreeSurferColorLUT.txt file has over 1,200 regions listed in it, but I assume that not all of those could be output in those default recon-all aparc+aseg* files. For example, I don't think I have ever seen a region: "3001wm-lh-bankssts 230 155 215 0" output. So, I ass

[Freesurfer] latest version of mri_glmfit-sim?

H ello Freesurfer Team, Where may I download the latest version of mri_glmfit-sim and QDEC to run the mri_surfcluster? I am having errors on mri_glmfit-sim and monte-carlo simulations in QDEC (dev version that was

Re: [Freesurfer] aparcstats2table

can you send the qdec file with variables? On 11/09/2016 11:51 AM, Martin Juneja wrote: > Hi Dr. Greve, > > Somehow even after adding variables, it's not working, although same > qdec file works fine when I perform GLM in qdec. > So I replaced the flag with subjectsfile and provided subject list

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

Donatas, please remember to include previous correspondence so that we have everything in one email. Can you upload your freesurfer subject so that I can debug it further? upload to https://gate.nmr.mgh.harvard.edu/filedrop2 On 11/09/2016 12:17 PM, Donatas Sederevicius wrote: > > I followed

[Freesurfer] Recon reprocessing control points error

Hi Bruce, Thanks for your email. I have uploaded the two examples. The first subj001_fs.zip has the control points added but has not been rerun yet. The second subj001_fs_cp.zip has been rerun and the segmentation looks incorrect. Thanks for your input! Sarah

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] aparcstats2table

Hi Dr. Greve, Somehow even after adding variables, it's not working, although same qdec file works fine when I perform GLM in qdec. So I replaced the flag with subjectsfile and provided subject list.txt file. So in that way, it's working fine now. I was also wondering (a) how can I average these

Re: [Freesurfer] Area after fsaverage resample

The "area" of a vertex is the average area of the triangles around the vertex. In fsaverage space, a vertex will map back to a given vertex in the individual subject, so the area of the vertex gets transferred back to fsaverage. And, yes, the area is measured in mm2. On 11/8/16 8:45 PM, Lac

[Freesurfer] mri_convert scaling

All, I have some DICOM files from a pet scan and an MRI. I viewed the files in three different ways: 1. Opened the DICOM's directly in a viewer (Pmod) 2. Used mri_convert to change the DICOMs to a .nii, and opened them. 3. Used dcm2nii to change the DICOMS to a .nii and opened them.

Re: [Freesurfer] nuisance dichotomous variables

I'm not sure what you mean. Dichotomous variables can be used. Our tutorial has an example of using gender. On 11/9/16 5:05 AM, Dominic Dwyer wrote: Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I wa

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

Was gtmseg.mgz created with the gtmseg script? On 11/9/16 4:43 AM, Donatas Sederevicius wrote: Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replac

Re: [Freesurfer] Recon reprocessing control points error

Hi Sarah if you upload the subject we will take a look. The best would be if you have upload the entire subject dir twice - once before and once after adding the additional control points Bruce On Wed, 9 Nov 2016, Sarah Finnegan wrote: Hi there,  I am using freesurfer v5.3.0 to recon some

Re: [Freesurfer] GM ROI list?

Sorry, I'm not sure what your question is here? On 11/8/16 5:25 PM, P Taylor wrote: OK, thanks for that list of complementary ROIs. I've always wondered what is the maximal set of regions that can be returned by the standard recon-all with no other options for aparc+aseg and aparc+aseg2009?

Re: [Freesurfer] aparcstats2table

Appears to be having problems reading the qdec table. It might be expecting the qdec table to actually variables in it. Can you try adding variables? Also, try it without the --qdec flag instead specifying the subjects with --subjects HC003_1 HC004_1 ... On 11/8/16 8:09 PM, Martin Juneja wrot

[Freesurfer] Recon reprocessing control points error

Hi there, I am using freesurfer v5.3.0 to recon some 7T structural scans. I have been adding some control points to compensate for poor temporal lobe contrast, something that has worked just fine many times before. However, now when rerunning the recon process as follows: recon-all -autorecon2-c

[Freesurfer] nuisance dichotomous variables

Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I was thinking that if it uses a generalized linear model then it should be ok? I read other posts and understand why discrete factors can't be used with mor

[Freesurfer] mri_gtmpvc error: failed tissue type check

Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue