[Freesurfer] vertices are -1 when using vol2label

External Email - Use Caution Hello! I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into a label so I tried: mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label but the resulting output file only has -1 as vertices. Is there anything wrong

[Freesurfer] convert to fsaverage

External Email - Use Caution Hello! I have a volumetric mask of the cuneus and I would like to convert it to a label and then convert that label to fsaverage space. So far I did mri_vol2label --i cuneus.nii.gz --l cuneus.label But how can I now convert cuneus.label to

Re: [Freesurfer] midsagittal mask

ute > it when we segment the callosum. You could set the lateral distance to > extend the callosum to 0 with -t 0 and then it will only label cc voxels in > the mid-sagittal plane > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] midsagittal mask

External Email - Use Caution Hello! I ran recon-all on my subject, is it possible to create a mask of the midsagittal plane using freesurfer? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] labels in anatomical space

.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sam W > *Sent:* Friday, June 3, 2022 10:46 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] labels in anatomical space > > > > *External Email - Use Caution* > > Hi Bruce, >

Re: [Freesurfer] labels in anatomical space

t; Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sam W > *Sent:* Friday, June 3, 2022 9:12 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] labels in anatomical s

[Freesurfer] labels in anatomical space

External Email - Use Caution Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] extracting BAs in freesurfer

External Email - Use Caution Hello! Is it possible to extract brodmann areas not included in the aparc? For example, BA9, BA10 and BA32? Thanks! Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Fwd: label to surface

External Email - Use Caution Hi! Just pinging. Is there a way to get the surface+overlay file as mentioned above using freesurfer? Thank you! Best regards, Sam -- Forwarded message - From: Sam W Date: Fri, Jul 10, 2020 at 9:05 PM Subject: Re: [Freesurfer] label

Re: [Freesurfer] label to surface

t's your mri_label2label command? > > On 7/10/2020 3:05 PM, Sam W wrote: > > External Email - Use Caution > Hi Doug and Tim, > I'm running probtrackx with freesurfer surfaces as seeds. However > probtrackx requires a file that contains both the whole surface file

Re: [Freesurfer] label to surface

or white surface. Best regards, Sam On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve wrote: > what do you mean merge with the pial? > > On 7/9/2020 8:07 PM, Sam W wrote: > > External Email - Use Caution > It works great Doug, thanks a lot! > Can I ask you a follow

Re: [Freesurfer] label to surface

to achieve that result? Best regards, Sam On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve wrote: > Use mri_label2label with the --outmask option > > On 7/8/2020 10:14 PM, Sam W wrote: > > External Email - Use Caution > Hi, > Is there a way to convert a label file i

[Freesurfer] label to surface

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] white vs pial target surface

External Email - Use Caution Hello, mri_vol2surf has the option to add a target surface (--surf) which can be the white (default) or pial surface. I get slightly different results depending on whether I use the white or pial surface as the target surface, so I was wondering in

Re: [Freesurfer] output of mri_surf2vol looks fragmented

, 2020 at 4:59 PM Douglas N. Greve wrote: > They will not look exactly the same. Try adding --ribbon ribbon.mgz > > On 7/6/2020 10:47 PM, Sam W wrote: > > External Email - Use Caution > Hi, > I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able

[Freesurfer] output of mri_surf2vol looks fragmented

External Email - Use Caution Hi, I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able to get the expected output when converting a surface back to volume. These are the commands I'm using: mri_vol2surf --mov lh_fusiform_pre.nii.gz --ref mri/orig.mgz --regheader

[Freesurfer] concatenate transformations

External Email - Use Caution Hello! I performed two registrations: diffusion-to-orig.dat and orig-to-rawavg.dat. Now I would like to concatenate the two transformation matrices into a diffusion-to-rawavg.dat. Is there a command in freesurfer that allows me to do that? Best

[Freesurfer] orig2rawavg transformation matrix

External Email - Use Caution Hello! How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I only see examples bringing freesurfer results into original anatomical space with mri_vol2vol, but I really just want the transformation matrix. Thanks! Best regards, Sam

[Freesurfer] dwi to native transformation

External Email - Use Caution Hello! I'm trying to create an fsl reg file that maps a dwi image to native anatomical space. 1. I used bbregister to create a reg file that maps the transformation from nodif to freesurfer's conformed space: bbregister --s sub001 --mov nodif.nii.gz

[Freesurfer] different target image for registration

External Email - Use Caution Hello! I would like to register my dwidata to the anatomical image (rawavg.mgz). I have run bbregister, but how can I specify a different target image? bbregister uses the orig.mgz right? These are the commands I used: bbregister --s sub001 --mov

[Freesurfer] registration of dwi images

External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my

Re: [Freesurfer] issue with lesions

v command. Try running that > to see if the registration is accurate. What is the nature of anat.nii? > > On 9/20/2019 4:41 PM, Sam W wrote: > > External Email - Use Caution > Thanks Doug, I'll try that. How would you register the lesion image (which > is anatomical

Re: [Freesurfer] issue with lesions

els in the lesion in orig.mgz with voxels from > orig.lrrev-in-orig.mgz and re-run > Let me know how it goes > > On 9/18/19 6:52 PM, Sam W wrote: > > > > External Email - Use Caution > > > > Thanks Doug. The problem is that for some patients the lesion affects

Re: [Freesurfer] issue with lesions

um lesions.sum.dat --thmin 0.5 > --regheader subject > This will output a list of lesions clusters in lesions.sum.dat and their > coordinates. you can see which ones are left and with ones are right. > > > > On 9/3/2019 5:17 PM, Sam W wrote: > > External Email - Use

[Freesurfer] issue with lesions

External Email - Use Caution Hello, I have run recon-all on T1 scans of patients with WM lesions. I noticed however that for some patients the lesion is excluded from aparc.a2009s+aseg.mgz but for other patients it is included (and labelled as non-lesion). Ultimately I'd like to

Re: [Freesurfer] label to asc

e surface, and also contains no > information about topology (e.g. which vertices are connected by an edge) > > cheers > Bruce > > > On Wed, 24 Jul 2019, Sam W. wrote: > > > > > External Email - Use Caution > > > > Thanks Bruce. Can I ask you a very basi

Re: [Freesurfer] label to asc

Bruce > On Tue, 23 Jul 2019, Sam W. wrote: > > > > > External Email - Use Caution > > > > Hi, > > > > Is it possible to convert a label file like rh.cuneus.label into asc? I > > tried > > mris_convert --label rh.cuneus.label ctx-rh-cuneus

Re: [Freesurfer] transformation question

, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Use lta_convert with --invert. BTW, the registration matrix is already > anat-to-diffusion > > On 7/22/2019 7:50 PM, Sam W. wrote: > > External Email - Use Caution > Thanks Doug! I'll use lta then, but which

[Freesurfer] label to asc

External Email - Use Caution Hi, Is it possible to convert a label file like rh.cuneus.label into asc? I tried mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc but got an error: ERROR: unknown file annot file type specified for output: rh.cuneus.asc

Re: [Freesurfer] transformation question

directionality. > > On 7/22/19 4:24 PM, Sam W. wrote: > > > > External Email - Use Caution > > > > Hi, > > I would like to create a registration matrix from orig.mgz to > > diffusion space. I created a reg file with > > > > bbregister

[Freesurfer] transformation question

External Email - Use Caution Hi, I would like to create a registration matrix from orig.mgz to diffusion space. I created a reg file with bbregister --t2 --init-fsl --reg /data/FS/sub01/reg.dat --mov /data/FS/sub01/B0.nii.gz --s sub001 but how can I invert this registration so

[Freesurfer] aseg annotation2label

External Email - Use Caution Hello, I'm trying to create label files of the aparc+aseg ROIs but cannot find the aseg annotations. The ?h.aparc.annot does not contain subcortical regions that exist in the aparc+aseg.mgz volume. Is there a way to apply mri_annotation2label to aseg

[Freesurfer] number of vertices

External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] check FS to native registration in freeview

ve to use the output of mri_label2vol in the freeview command > > On 5/13/2019 5:02 PM, Sam W. wrote: > > External Email - Use Caution > Hi, > > After bbregister, I ran mri_label2vol to convert a segmentation file to > native functional space > > mri_label2vol --seg s

[Freesurfer] check FS to native registration in freeview

External Email - Use Caution Hi, After bbregister, I ran mri_label2vol to convert a segmentation file to native functional space mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o aseg-in-func.nii --temp example_func.nii Now I would like to check how well the

Re: [Freesurfer] convert aseg to functional space

istration actually goes from anat to func. mri_label2vol knows > this. In any case, it is just a matrix that can easily be inverted. > > On 4/18/19 11:58 AM, Sam W. wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > Thanks! After registering w

Re: [Freesurfer] convert aseg to functional space

> (mri_vol2vol) so that it is in registration with the anatomical; > transferring it to anat space handles partial voluming better. > > On 4/16/19 8:21 PM, Sam W. wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I just finished

[Freesurfer] convert aseg to functional space

External Email - Use Caution Hi, I just finished reconall and now I'd like to convert the aseg.mgz to native functional space. My first thought was to simply convert the aseg.mgz to native functional space with mri_vol2vol: mri_vol2vol --mov sub001/mri/aseg.mgz --targ

[Freesurfer] same aparc ROI with mri_label2vol?

External Email - Use Caution Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label

Re: [Freesurfer] same output with vol2vol and label2vol

:12 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Are they exactly the same? Try > mri_diff file1.mgz file2.mgz > I would not expect them to be all that different, just a few voxels here > and there > > On 4/16/19 3:47 PM, Sam W. wrote: > > > >

[Freesurfer] same output with vol2vol and label2vol

External Email - Use Caution Hi, In a Freesurfer help webpage it says that to convert an image (eg brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use mri_label2vol. I converted the

[Freesurfer] problems with bbregister's output image

External Email - Use Caution Hello, I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2. $ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2