Re: [Freesurfer] mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)

Can you confirm that /subjects/CI_01/mri/orig.mgz exists? Usually, your  SUBJECTS_DIR would not be directly in root, especially on a mac, but it is not impossible. On 10/14/2022 7:17 AM, Wandschneider, Britta wrote: External Email - Use Caution Hello, I am trying to map

[Freesurfer] mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)

External Email - Use Caution Hello, I am trying to map tumour+oedema lesion masks (generated with ITKSnap) to subjects' freesurfer surface (in native space) using mri_vol2surf. This is an example of the command I am using for a specific subject: mri_vol2surf --mov

Re: [Freesurfer] mri_vol2surf error

Pick a hemisphere (either lh or rh). Also, you should verify that your volume overlays on fsaverage correctly with something like tkmeditfv fsaverage orig.mgz -surfs -fminmax .01 1 -ov rReslice_Combined_roi_meanRD.nii  -reg $FREESURFER_HOME/average/mni152.register.dat On 7/11/2022 6:23 PM,

[Freesurfer] mri_vol2surf error

External Email - Use Caution Hello everyone, I am trying to display my lesion map I created in Matlab on a cortical surface, and am getting the following error: developer@developer-VirtualBox:~$ mri_vol2surf --mov rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject

[Freesurfer] mri_vol2surf with --projopt

External Email - Use Caution Dear FreeSurfer experts, I have a question on the usage of mri_vol2surf's option, "--projopt". What I want to do is to map the diffusion scalar value (like mean diffusivity [MD]) to the cortical surface. Though mri_vol2surf with --projfrac 0.5 worked

Re: [Freesurfer] mri_vol2surf clarification

Sorry, I don't understand what you are trying to do. Extract ROI (eg, hippocampal) time courses? On 9/14/2021 4:29 AM, Alice Giubergia wrote: External Email - Use Caution Dear Freesurfer's experts, I am dealing with time course extraction from preprocessed (prerpoc-sess) task

[Freesurfer] mri_vol2surf clarification

External Email - Use Caution Dear Freesurfer's experts, I am dealing with time course extraction from preprocessed (prerpoc-sess) task functional data; I was able to extract the time courses from the fsaverage sampled surfaces fmcpr.up.sm3.fsaverage.lh.nii.gz thanks to

[Freesurfer] mri_vol2surf empty output

External Email - Use Caution Hi FS Forum, I am posting because after using the command mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf --src bold_preproc.nii.gz --out

Re: [Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

Yes, 2x the thickness On 3/10/2021 11:17 PM, Horn, Mitchell Jacob wrote: Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM

[Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM boundary? Thanks in advance! Mitch

Re: [Freesurfer] mri_vol2surf resolution warning

That registration assume that the input is the MNI152 volume with 1mm voxel size. This still might work, but I would check the registration between the 1mm MNI152 and the 6mm volume On 2/26/2021 12:35 PM, Russo, Andrew William wrote: Hello, I am moving a 6mm volume from MNI152 to fsaverage

[Freesurfer] mri_vol2surf resolution warning

Hello, I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get the following warning: mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh --interp nearest --surf-fwhm 4 WARNING: the voxel resolution in the source volume (6,6,6) differs from

[Freesurfer] mri_vol2surf

External Email - Use Caution Hello, I am trying to run mri_vol2sur to obtain the AAL atlas on freesurfer. i used this command line "mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img"

[Freesurfer] mri_vol2surf

External Email - Use Caution Hello, I have a couple of questions: 1. I asked before how to obtain AAL labels on Freesurfer. I am following your instructions, but I don't know how to load the AAL onto my T1w template to ensure everything aligns 2. Secondly, I tried to run

Re: [Freesurfer] mri_vol2surf MRISread error

Does that file exist? What is your $SUBJECTS_DIR? Can you send the full terminal output? On 10/4/2020 2:05 AM, KN Qiao wrote: External Email - Use Caution Hello FreeSurfer Developers, mri_vol2surf --mov $mask_dir/rest_brainmask.nii.gz --reg $reg_dir/rest2t1.dat --trgsubject fsaverage

[Freesurfer] mri_vol2surf MRISread error

External Email - Use Caution Hello FreeSurfer Developers, mri_vol2surf --mov $mask_dir/rest_brainmask.nii.gz --reg $reg_dir/rest2t1.dat --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi ${hemi} --o ${mask_dir}/mask.fsaverage.${hemi}.nii.gz --noreshape --cortex

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

t; Reply-To: Freesurfer support list Date: Monday, June 29, 2020 at 1:11 PM To: Freesurfer support list , "freesurfer-boun...@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion External Email - Use Caution Yes you are probably low on memory

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

Wells Reply-To: Freesurfer support list Date: Monday, June 29, 2020 at 12:50 PM To: Freesurfer support list , "freesurfer-boun...@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion External Email - Use Caution Hi Matt, I have 3.5GB fre

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

Ffôn: 02920 879628 From: on behalf of "Glasser, Matthew" Reply to: Freesurfer support list Date: Monday, 29 June 2020 at 17:28 To: Freesurfer support list , "freesurfer-boun...@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

. Matt. From: on behalf of "Glasser, Matthew" Reply-To: Freesurfer support list Date: Monday, June 29, 2020 at 11:24 AM To: Freesurfer support list , "freesurfer-boun...@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

support list Date: Monday, June 29, 2020 at 11:20 AM To: "freesurfer-boun...@nmr.mgh.harvard.edu" , Freesurfer support list Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion External Email - Use Caution Dear experts, I posted a message last week about converting N

[Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution Dear experts, I posted a message last week about converting NIFTI files into GIFTI format, then GIFTI to CIFTI, whilst keeping these functional data in the same space as the subjects FS surface. I got some information RE usign the HCP workbench, but

Re: [Freesurfer] mri_vol2surf

Try this version (for linux) https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf If you run it without any arguments, it will print help. At the very end you will see a flag called --vol2surf On 5/30/2020 11:08 AM, Nasr, Shahin,Ph.D. wrote: Hi Surfers,     Is there anyway to pass

[Freesurfer] mri_vol2surf

Hi Surfers, Is there anyway to pass the full address of a surface to mri_vol2surf? To clarify, we are using surfaces that are saved outside /surf/ and we prefer not to relocate them every time that we want to use mri_vol2surf. Thanks ___

Re: [Freesurfer] mri_vol2surf projections for subcortical structures

Hi Niels I don't see why not. vol2surf takes the surface location and the surface normal and sampled from the volume onto the surface using those two pieces of local information. Global surface topology shouldn't matter cheers Bruce On Sun, 29 Mar 2020, Niels Janssen . wrote:

[Freesurfer] mri_vol2surf projections for subcortical structures

External Email - Use Caution Dear list I am working on a project in which we want to extract hippocampal surfaces using mri_tessellate and then overlay these surfaces with fmri activations from nifti files using mri_vol2surf. However, I am unclear whether mri_vol2surf can be used

Re: [Freesurfer] mri_vol2surf produces invalid surface

External Email - Use Caution Thanks a lot. Now I understand what was wrong and resolve it. Shuntaro 2020年2月29日(土) 6:20 Douglas N. Greve : > > mri_vol2surf does not actually produce a surface, it produces a surface > overlay (ie, a value for each vertex). You can to run

Re: [Freesurfer] mri_vol2surf produces invalid surface

mri_vol2surf does not actually produce a surface, it produces a surface overlay (ie, a value for each vertex). You can to run recon-all to produce a surface On 2/27/2020 4:49 AM, Shuntaro Aoki wrote: > External Email - Use Caution > > Dear mailing list, > > I was trying to convert a

[Freesurfer] mri_vol2surf produces invalid surface

External Email - Use Caution Dear mailing list, I was trying to convert a volume image to a freesurfer surface (as gii) with `mri_vol2surf` for visualization, but ended up with invalid surface data (i.e., a file not loadable by freeview). What I did was: --- % mri_vol2surf

Re: [Freesurfer] mri_vol2surf fails

Are those values actually 0 or just very small? Is that area dark on the T2*? On 8/26/19 11:20 AM, Sackl, Maximilian wrote: > External Email - Use Caution > > Thank you for the prompt answer! > > No, the T2* map within the pial and WM does include values ... > Any ideas? > > On

Re: [Freesurfer] mri_vol2surf fails

You should bring up the T2* with the surfaces. Is it possible that the T2* just did not include that particular bit? On 8/26/19 10:38 AM, Sackl, Maximilian wrote: > External Email - Use Caution > > Dear FreeSurfer experts, > > I was trying to perform a GLM fit with T2* data, projected

Re: [Freesurfer] mri_vol2surf error

Not ssure what is happening. CAn you send the full terminal output. Also, remove the --out_type flag. No need to include --surfreg sphere.reg (but should not hurt anything). On 8/14/19 12:37 PM, Pratik Kashyap wrote: > > External Email - Use Caution > > mri_vol2surf --cortex --hemi lh

[Freesurfer] mri_vol2surf error

External Email - Use Caution mri_vol2surf --cortex --hemi lh --interp trilinear --o rest2.nii.gz --out_type niigz --reg register.dat --projfrac-avg 0.500 --mov rest2.nii --surfreg sphere.reg --trgsubject fsaverage A source volume path must be supplied Hey, I'm running the

Re: [Freesurfer] mri_vol2surf for functional 4D BOLD data only mapping 1 frame

did you check the output? I think it should have the appropriate number of frames. You can use mri_info to check the dimensions On 5/13/2019 7:35 AM, Robert Austin Bruce Benn wrote: External Email - Use Caution Hi There, I’m currently trying to run mri_vol2surf on some animal data and

[Freesurfer] mri_vol2surf for functional 4D BOLD data only mapping 1 frame

External Email - Use Caution Hi There, I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve been working with. I’m having a bit of a problem with the command mri_vol2surf. I seem to be able to project my functional volume to my surface, however I’m

[Freesurfer] mri_vol2surf error

External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am

Re: [Freesurfer] mri_vol2surf error

External Email - Use Caution Dear Doug Greve, Sorry, issue solved! I had used a wrong path directory in the commandline... it’s now working perfectly well. Thanks for your help, Sincerely, Loïc Daumail Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <

Re: [Freesurfer] mri_vol2surf error

can you send the full terminal output of the mri_surf2vol command? On 4/17/19 5:59 AM, Loïc Daumail wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I am currently trying to use mri_vol2surf on my bold data. I typed > this commandline : > " > mri_vol2surf --mov >

[Freesurfer] mri_vol2surf error

External Email - Use Caution Dear Freesurfer experts, I am currently trying to use mri_vol2surf on my bold data. I typed this commandline : " mri_vol2surf --mov ${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz \ --mni152reg \

Re: [Freesurfer] mri_vol2surf sample inside and outside of pial

yes, although note that neither one is guaranteed to be "inside" or "outside" at that distance (it might reenter the surface in the outwards normal direction, or leave the surface in the inwards direction) cheers Bruce On Tue, 5 Mar 2019, Michael Jordan wrote: External Email - Use

[Freesurfer] mri_vol2surf sample inside and outside of pial

External Email - Use Caution Hi, I have a short question concerning the mri_vol2surf command. Do the following parameters of the command return the maximum volume value (for each vertex) which occurs between 10 mm outside and 10 mm inside the pial surface (along normal vector)?

Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

Hi Michael you can use either --projfrac-avg or --projdist-avg (dist I guess if you want to specify 10mm). Note that this is an average along 1D (the surface normal direction), not in a volume window cheers Bruce On Wed, 27 Feb 2019, Michael Jordan wrote: External Email - Use

Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

External Email - Use Caution Hi Bruce, thank you it worked! Another short question: I want mri_surf2vol to assign the average of all volume voxel values within 10 mm to the corresponding vertices. So if there is only one voxel value greater than zero in the volume, all vertices

Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

Hi Michael you can use --regheader, which uses the ras2vox matrices to compute the registration (which is also what freeview does). cheers Bruce On Mon, 18 Feb 2019, Michael Jordan wrote: External Email - Use Caution Hi, i would like to sample the t-values of a SPM

[Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

External Email - Use Caution Hi, i would like to sample the t-values of a SPM output volume (spmT_0001.nii) onto the pial surface of the same subject. The volume is already aligned to the surface files (so if I view the volume as well as the surface files in Freeview they are

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

External Email - Use Caution Hello Bruce, As suggested by you, I used tkmeditfv to view the volumetric maps on the surface and it seems like the dACC cluster is lying outside the brain. I checked the registration of the volumetric file using tkregisterfv but surprisingly nothing

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

you can try tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3 you may have to adjust the thresholds (fminmax) On 6/26/18 10:43 PM, srishti goel wrote: External Email - Use Caution Hello Bruce, You had mentioned about loading the volumetric maps with the surface

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

External Email - Use Caution Hello Bruce, You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

External Email - Use Caution Hi Bruce, Thank you so much for your prompt help. Can I achieve that with: tkregisterfv --mov [your volume maps] --regheader --s [the subject on whose surface map is registered] --surfs --reg [file name] Best, Srishti Best, Srishti Social/Clinical

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

Hi Srishti you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface. cheers Bruce On Mon, 25 Jun 2018, srishti goel wrote: External Email - Use Caution They are separate clusters not the same

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

External Email - Use Caution They are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both? On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a

[Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface. Is that because dACC/insula is not included in surfaces on

Re: [Freesurfer] mri_vol2surf projection

You should first make sure that the registration is ok with tkregister --mov ICA_split.nii.gz --regheader --s fsaverage5 --reg deleteme.dat Note that going from a volume group space onto the surface is often not that good On 06/11/2018 11:45 AM, Tom Vanasse wrote: > > External

[Freesurfer] mri_vol2surf projection

External Email - Use Caution Hello, I wanted to confirm that I properly performed the mri_vol2surf command. I'm interested in projecting a z-score image (in Talairach space) to an average surface (fsaverage5), using a mid-gray projection fraction. mri_vol2surf --src

Re: [Freesurfer] mri_vol2surf

Hi,Yes the longitudinal images after the long run are all aligned in the base space. You will find the map from each time point to the base in the base MRI transforms dir (maybe also in the long MRI transforms). Naming should make clear what reach one is.Best MartinAm 09.05.2018 21:11 schrieb

Re: [Freesurfer] mri_vol2surf

There is a registration file that gets created by the longitudinal processing that can be used with mri_vol2vol. I don't know where the LTA file is, but maybe Martin can weigh in. On 05/08/2018 12:31 PM, Abdullah Ishaque wrote: > > > Hi, > > I figured that part out: I can't load surfaces as

Re: [Freesurfer] mri_vol2surf

External Email - Use Caution Hi, I figured that part out: I can't load surfaces as volumes in freeview, but rather i need to load them as an overlay to the subject white, or pial surfaces. I have another question for which I can't find an answer to. After registering myelin maps

Re: [Freesurfer] mri_vol2surf warning

And what is the voxel resolution of the input to mri_vol2surf? On 05/02/2018 03:35 PM, Rachel Bencic wrote: > > > Hello, > > The voxel resolution of the unwarped mov volume used in bbregister was: > > voxel sizes: 3.75, 3.75, 5.00 > > So the reported values in the warning appear

Re: [Freesurfer] mri_vol2surf warning

When you ran bbregister, what was the voxel resolution of the mov volume? On 05/02/2018 01:28 PM, Rachel Bencic wrote: > > > Hello FreeSurfer Developers, > > I'm attempting to resample beta weights generated from AFNI’s > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior >

[Freesurfer] mri_vol2surf warning

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to resample beta weights generated from AFNI’s 3dDeconvolve command to individual subjects’ cortical surfaces. Prior to running 3dDeconvolve, I ran bbregister to coregister subjects’ (unwarped) functional

Re: [Freesurfer] mri_vol2surf

External Email - Use Caution I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5 Now I'm just getting the error "freadFloat: fread failed" a whole bunch of times and the terminal gets stuck. Any suggestions? I checked

Re: [Freesurfer] mri_vol2surf

Specify a file format for the output (eg, C01.mgz) On 4/24/18 3:17 PM, Abdullah Ishaque wrote: External Email - Use Caution Hi, Thank you for the prompt response. I used the following command: mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the

Re: [Freesurfer] mri_vol2surf

External Email - Use Caution Hi, Thank you for the prompt response. I used the following command: mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5 This created two files called

Re: [Freesurfer] mri_vol2surf

That all looks correct. For the registration, just use --regheader C01 On 4/24/18 11:12 AM, Abdullah Ishaque wrote: Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart

[Freesurfer] mri_vol2surf

External Email - Use Caution Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject,

[Freesurfer] mri_vol2surf: issue with registration

Hi , I am facing an issue when I try to compare two network-based maps, one of which has been registered on a surface while the other one has not. If anyone has tried doing something similar and has any thoughts about it please share your suggestions, I highly appreciate it. I have two sets of

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Hi Srishti, you will need to be much more specific to allow me to help you. mni152_subject is not a file that can be input to recon-all (it should be a dicom or nifti or mgz). If you use the same input to recon-all that you used to view it in spm, then the FS output should align with your map.

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

What is the "MNI template" that you are using. I mean an exact file used. Did you use this file when you ran recon-all? On 04/12/2018 10:23 AM, srishti goel wrote: > Yeah, I am unsure where to go from here as well. So the results can be > viewed in SPM and on the MNI template space itself,

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Yeah, I am unsure where to go from here as well. So the results can be viewed in SPM and on the MNI template space itself, since SPM typically does not have a problem showing multiple images in different sizes. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

don't use --init-rr ( you don't need to spec an init in version 6) On 4/10/18 9:48 PM, srishti goel wrote: When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii. No such file or directory Any help is

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader On 4/9/18 11:49 PM, Bruce Fischl wrote: How did you generate the registration? And give us the details of what you are trying to register Cheers

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce > On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote: > > Hi Bruce, > > Thanks so much for pointing that out, I totally missed that part. > > Also, the

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

When I type this command: tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to

[Freesurfer] mri_vol2surf: unable to compare volume maps

Hi, I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows: Commands: mri_vol2surf --src negative_allsocial_proportion.nii

Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

Hi Doug, great, this works well, thank you very much! Best Charlotte - Original Message - From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 14, 2018 11:37:13 PM Subject: Re: [Freesurfer] mri_vol2surf - what r

Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

You should be able to use --regheader ANTSaverage (assuming ANTSaverage is the name you gave it when running recon-all) On 03/12/2018 01:32 PM, Charlotte Grosse Wiesmann wrote: > Hi Doug, > > I was trying to map my volume mask from my study-specific average subject > template space to the

[Freesurfer] mri_vol2surf - what register.dat file to use?

Hi Doug, I was trying to map my volume mask from my study-specific average subject template space to the surface (still in my average subject template space) with mri_vol2surf as you suggested below. How d I get the correct register.dat file do do this? I have tried bbregister but am not sure

Re: [Freesurfer] mri_vol2surf wrong hemisphere

11:46:27 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere How do you know what is right and left in the volume? On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote: > > Hi, > > I have a strange issue I can't figure out. I am currently trying t

Re: [Freesurfer] mri_vol2surf wrong hemisphere

How do you know what is right and left in the volume? On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote: > > Hi, > > I have a strange issue I can't figure out. I am currently trying to > use the parcellation from Gordon et al. 2014 > (http://www.nil.wustl.edu/labs/petersen/Resources.html)

[Freesurfer] mri_vol2surf wrong hemisphere

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public

[Freesurfer] mri_vol2surf wrong hemisphere

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (download link here) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152

Re: [Freesurfer] mri_vol2surf

probably youu'll want to sample it in the middle of the cortical ribbon, so --projfrac 0.5 On 8/22/17 12:11 PM, John Anderson wrote: Thank you for the response It is FDG SUV map need more info, eg, what kind of map is that? what modality? Original Message Subject:

Re: [Freesurfer] mri_vol2surf

> Thank you for the response > > It is FDG SUV map > > need more info, eg, what kind of map is that? what modality? > >> Original Message >> Subject: mri_vol2surf >> Local Time: August 22, 2017 11:04 AM >> UTC Time: August 22, 2017 3:04 PM >> From: john.ande...@protonmail.com >>

Re: [Freesurfer] mri_vol2surf

need more info, eg, what kind of map is that? what modality? On 8/22/17 11:04 AM, John Anderson wrote: Dear FS experts, I ran voxel-wise analysis between two groups using randomise in FSL and the final statistical maps is as attached. I aim to to repeat the analysis using surface based

[Freesurfer] mri_vol2surf

Dear FS experts, I ran voxel-wise analysis between two groups using randomise in FSL and the final statistical maps is as attached. I aim to to repeat the analysis using surface based analysis. I followed the steps as in wiki. I am not sure what is the correct value for projfrac int he command

Re: [Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

Hi Freesurfer Team, No worries, I have found a helpful solution from an old thread using mris_expand. http://i.imgur.com/CrF125X.png Thanks. Best Wishes, Elijah On Tue, Jun 13, 2017 at 8:47 PM, Elijah Mak

[Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

Hi Freesurfer Team, Is there a way to visualise the sampling edges across a range of projfrac values (0.1 (closer to WM) - 0.5) and overlay them onto PET data? Any suggestions are greatly appreciated. Thanks. Best Wishes, Elijah  ___ Freesurfer

Re: [Freesurfer] mri_vol2surf error in FS6

> > Thanks so much > > > > > > > > joseph > > > > > > > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado > > <ladof...@gmail.com <mailto:ladof...@gmail.com> > > > <mailto:

Re: [Freesurfer] mri_vol2surf error in FS6

> <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>> > > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com> > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>>> wrote: > > > > >

Re: [Freesurfer] mri_vol2surf error in FS6

> <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>> wrote: > > > > > > yes, I have the /Applications/freesurfer/lib/gcc > > > directory.(actually, ‘had’ as I reinstalled 5.3) I installed > 6.0 > >

Re: [Freesurfer] mri_vol2surf error in FS6

..@gmail.com <mailto:ladof...@gmail.com>>> wrote: > > > > yes, I have the /Applications/freesurfer/lib/gcc > > directory.(actually, ‘had’ as I reinstalled 5.3) I installed 6.0 > > on top of 5.3 without uninstalling

Re: [Freesurfer] mri_vol2surf error in FS6

I installed 6.0 > > on top of 5.3 without uninstalling 5.3 first, so it was not a clean > > install. I will try a clean re-install with the tar file with the > > steps you suggest. Thanks. > > > > Date: Sun, 5 Mar 2017

Re: [Freesurfer] mri_vol2surf error in FS6

I installed 6.0 > on top of 5.3 without uninstalling 5.3 first, so it was not a clean > install. I will try a clean re-install with the tar file with the > steps you suggest. Thanks. > > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST) > From: zkauf...@nmr.mgh.harv

Re: [Freesurfer] mri_vol2surf error in FS6

22:01 -0500 (EST) > From: zkauf...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_vol2surf error in FS6 > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <62233.174.63.82.222.14887

Re: [Freesurfer] mri_vol2surf

Thank you very much Douglas, You made my day ! Have a good day, Redwan On 14 March 2017 at 10:48, Douglas Greve wrote: > Yes, I see a spot on the medial wall. You can also look at it in the > volume with > > tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay

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