Re: [Freesurfer] Patlak PET/MRI

On 1/28/2025 12:51 PM, Andrade Rey René wrote: External Email - Use Caution Dear community, I have tried the tutorial for PETsurfer. I would like to ask some questions. 1) I have seen in the tutorial when you do PVC correction it is done on PET dynamic raw data. Is this correct?

Re: [Freesurfer] Automated extraction of dural/meningeal ROI

In that post, I'm not saying that we have a meninges segmentation, just that the meninges might be removed when doing skull stripping. This will not remove the signal from meninges that has partial-volumed into the brain. We don't have a way to do that unless there is a meningeal ROI. On 1/30/

Re: [Freesurfer] Subcortical under segmentations

Hippcampus actually looks like it might be ok; are those holes actually ventricle? I don't see a caudate label on there. Thalamus can often be underlabeled as there is so much WM in it. You can try running the thalamic nuclei segmentation, eg, segment_subregions thalamus --cross subject This wi

Re: [Freesurfer] longitudinal analysis on one subject

The glm can be run on this data in theory. With only 5 time points, you probably won't have much power though. What are you trying to test? On 2/1/2025 11:56 PM, Isabella Rossellini wrote: External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1

Re: [Freesurfer] Error in loading wmparc2diff.mgz

Does that file exist? On 2/2/2025 11:34 AM, Ramesh Babu wrote: External Email - Use Caution Dear Experts, May I know why wmparc2diff is unreadable? Please suggest. Thank you Ramesh On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu wrote: Dear Yujing, For the command, freevi

Re: [Freesurfer] Corpus Callosum Missing in SAMSEG Output

samseg does not have a CC seg. You can get the CC with something like mri_cc -aseg samseg/seg.mgz  -o samseg/seg+cc.mgz -lta samseg/cc_up.lta you can ignore the lta output On 1/28/2025 7:00 PM, Taghizadeh Mortezaei, Nima wrote: Dear FreeSurfer Support Team, I am using FreeSurfer version 7.4.1

Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, January 28, 2025 12:41 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation Try using recon-all-clinical.sh

Re: [Freesurfer] FreeSurfer 8.0.0 beta error, while calculating the local gyrification index

This is a known issue when recon-all v8-beta is run a 2nd time. It will be fixed in the final v8 release. In the mean time, you can get around it with cd $SUBJECTS_DIR/subject/surf mris_compute_lgi --i lh.pial mris_compute_lgi --i rh.pial On 1/27/2025 5:59 AM, Katharina Wittfeld wrote:

Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation

Try using recon-all-clinical.sh; it works a lot better on these thick slice data On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote: Hello FreeSurfer Developers and Community, I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resample

Re: [Freesurfer] Identical values for different cingulate regions

It is hard to say without the data. I checked one of our cases and they are different, although it was not from v6 (but I would not expect this to change). Can you try running it in a newer version? Or re-run in v6? On 1/27/2025 1:42 AM, Taghizadeh Mortezaei, Nima wrote: Dear FreeSurfer devel

Re: [Freesurfer] fixing/editing white matter surface

You can edit the brain.finalsurfs.manedit.mgz to remove those voxels. You may need to removed them from the wm.mgz and filled.mgz On 1/21/2025 1:41 PM, Eszter Boros wrote: External Email - Use Caution Dear FreeSurfer Team, We are editing some longitudinal data using FreeSurfer 7.4.1

Re: [Freesurfer] longitudinal analyses, more than 2 timepoints

you can use the two stage model On 1/15/2025 1:52 PM, Eszter Boros wrote: External Email - Use Caution Dear FreeSurfer Team, We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and

Re: [Freesurfer] recon-all error

It says that it cannot find /run/media/user/2TB/freesurfer/ASegStatsLUT.txt does that file exist on your system? On 1/16/2025 6:20 PM, 박경일 wrote: External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the

Re: [Freesurfer] [freesurfer] recon-all error

it says finished without error On 1/15/2025 5:13 PM, 박경일 wrote:     External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I’ve experienced an issue with this routine process. Please refer to the

Re: [Freesurfer] aseg.mgz file not generated after recon-all

That flag is to perform only the subcortical segmentation, but there are are steps leading up to it that need to be done. If all you want is a subcortical seg, then you can just run mri_synthseg --i orig.mgz --o synthseg.mgz On 1/15/2025 8:42 AM, Sara Rapuc wrote: External Email - U

Re: [Freesurfer] Recon-all error...

That recon-all.log file says it returned without error: "recon-all -s E0001 finished without error at Mon Dec 23 12:20:40 KST 2024" what's the problem? On 1/13/2025 10:26 PM, 박경일 wrote: External Email - Use Caution Dear FS Development Team, I recently encountered an error while runn

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

Sorry, I deleted the original thread. Can you remind me of the original problem? On 1/13/2025 4:51 PM, Michael Eyre wrote: External Email - Use Caution Hi, thanks for your response, apologies for late reply. nu.mgz looks fine When I run tkregisterfv --s subject --fstal :  orig.mgz(

Re: [Freesurfer] New user

welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See https:/

Re: [Freesurfer] Any updates on thalamic nuclei mask in MNI space?

That is probably the best way. Another way would be to run the seg on a set of subjects, run fs-synthmorph-reg on those subjects (non-lin reg to mni152), then map the individuals thal segs to mni, then combine them together. Not sure which one is base. Certainly just running the thal seg on the

Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: Error in recon-all

difference in the files? On Wed, Jan 8, 2025 at 8:01 AM Douglas N. Greve wrote: I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag? On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote: External Email - Use C

Re: [Freesurfer] copy headers

You can try something like mri_convert --in_like template.mgz yourfile.mgz yourfile2.mgz On 1/7/2025 3:28 PM, Aaron Tanenbaum wrote: External Email - Use Caution Hello All, Is there a FreeSurfer tool that will copy header information from one image to the other with the same dimensi

Re: [Freesurfer] Error in recon-all

I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag? On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote: External Email - Use Caution You are correct. Attached is the correct one On Tue, Jan 7, 2025 at 8:08 AM Douglas N.

Re: [Freesurfer] Error in recon-all

Are you sure this is the right recon-all.log file? At the end it says it finished without error On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote: External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The r

Re: [Freesurfer] registration error

You have to pass it the name of the subject with the --s flag. The subject name is that produced by recon-all -s subject ... On 1/4/2025 7:30 AM, Ramesh Babu wrote: External Email - Use Caution Hello, I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local subject spa

Re: [Freesurfer] How to Plot Surface with ROI Boundaries Using Harvard-Oxford Brain Atlas?

I'm not sure what you are trying to do. The HO atlas is volume-based, isn't it? On 1/3/2025 4:41 PM, Zeng, Xinglin wrote: External Email - Use Caution Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My g

Re: [Freesurfer] (no subject)

;. Another uncommon thing is that, after loading the surfaces, it gives me an error about the reconstruction of the inverse matrix... Il Mer 1 Gen 2025, 23:28 Douglas N. Greve ha scritto: Hard to say from those images. In the 2nd, the surface is no where near where it should be -- it

Re: [Freesurfer] How Can I Track Coordinates from NIfTI Raw Files

Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 12/22/2024 11:05 PM, 권용현 wrote: External Email - Use Caution Hello, I am conducting research using ECoG. I want to accurately track the location of electrodes. I am inputting data from a NIfTI fil

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

For sub-04, can you look at the nu.mgz volume to see if that looks ok? Can you also see if the talairach registration looks ok? You should be able to run something like tkregisterfv --s subject --fstal It does not have to be perfect, but it is a problem if it is wildly off. On 12/29/2024 10:

Re: [Freesurfer] Reliability of Optic Chiasm Volume Measurements in FreeSurfer

I don't know that anyone has ever really looked at it. It is hard to define the volume for it as it is just the crossing point of the optic nerves. On 12/29/2024 6:26 AM, Knut J Bjuland wrote: External Email - Use Caution Dear FreeSurfer experts, I am examining the optic chiasm seg

Re: [Freesurfer] (no subject)

Hard to say from those images. In the 2nd, the surface is no where near where it should be -- it looks like it is misregistered with respect to the brain (that not an intensity problem). What is your freeview command to view the images? On 12/23/2024 8:17 AM, Tommaso Mariani wrote:

Re: [Freesurfer] Extracting just the eTIV from stats file.

When you say that it doesn't work, what do you mean? I was able to run your command line successfully in 7.1.1 On 12/18/2024 7:34 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi guys, I need to extract the eTIV from a stats file Its like this

Re: [Freesurfer] [External] Re: Subject: query about mri_vol2surf

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, December 10, 2024 11:43 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Subject: query about mri_vol2surf You don't often get email

Re: [Freesurfer] obtain vertex neighborhood

Use mris_info, eg mris_info --vx 1000 lh.white vertexno 1000 xyz  -21.1794 -74.9562 37.7794 nxyz  0.9807  0.1533 -0.1214 vertex_area 0.661364 neighbors 6 6 nbr 0    748 0.7216 0.5103  1944 0.2824 nbr 1  102418 0.9059 0.5654  1945 0.2912 nbr 2    991 0.7688 0.4739  2578 0.3172 nbr 3    992 0.9298

Re: [Freesurfer] Single voxel grey-white matter boundary binary mask

You can use mri_surf2vol with the --mkmask option (method 2; see mri_surf2vol --help), eg, cd subject/surf mri_surf2vol --mkmask --hemi lh --o mask.lh.mgz --identity subject --template ../mri/nu.mgz If you want to go to another volume, supply the registration to that volume with --reg instead o

Re: [Freesurfer] Spiky Brains

This sometimes happens with noisy data. The difference in SNR between those two scans is a factor of 2. What is your recon-all command line? Can you send pics of the brain image with the surface overlaid on a slice with one of the spikes? What does the white surface look like in those regions?

Re: [Freesurfer] Freesurfer v8.0.0 error

I think this is the bug where you need to set the environment variable  FS_ALLOW_DEEP to 1, eg,  export  FS_ALLOW_DEEP=1 or  setenv FS_ALLOW_DEEP 1 Try that and then rerun On 12/11/2024 12:14 PM, Huang, Yujing wrote: Can you add those options as shown in the output ‘-fix-ento-wm -transfer-bas

Re: [Freesurfer] Petsurfer: PET -> MNI305 problem

Yes, this  is a bug. I have fixed it in our development version. For now, you can use your workaround. On 12/7/2024 1:28 AM, Shen, Qian wrote: External Email - Use Caution Hi Dr. Greve and Experts, I encountered an issue while running the following command to resample meltzer.nii.gz

Re: [Freesurfer] recon-all on poor MRI quality

It is probably indirectly related to the large slice thickness. You might try running recon-all_clinical.sh On 12/10/2024 11:28 AM, Francesco Lomi wrote: > External Email - Use Caution > > Dear all, > I am writing you because I would like to know why recon-all on this > subject exited w

Re: [Freesurfer] Questions about CVS registration

You can invert the gca with somehting  like mri_ca_register -invert-and-save cvs.gca inv.cvs.gca The apply inv.cvs.gca  to map from CVS space back to the native space On 12/6/2024 3:51 AM, Tanxin Dong wrote: External Email - Use Caution To whom this may concern: Hi, I’ve been working

Re: [Freesurfer] Subject: query about mri_vol2surf

For mapping to the surface, each surface vertex has an xyz coordiate in anatomical space. The registration file is used to convert this into the column, row, slice in the overlay space. The value of the overlay volume at the CRS is then assigned to that vertex. In your case, the coordinate is a

Re: [Freesurfer] Recon all across different image dimensions of different clinical subjects!

On 12/5/2024 10:14 PM, JM wrote: External Email - Use Caution Hi FreeSurfer experts, In our hospital research settings, we collected structural MRI data from patients while they were admitted for treatment. Some of the patients were scanned before contrast agent was injected and s

Re: [Freesurfer] Take screenshot via sbatch without launching GUI

You can use a virtual frame buffer. I wrote a frontend for one to do just this here is the help # fsxvfb - a simple application of the virtual frame buffer (vrb) for # X This can run graphical commands in a "headless" way, ie, without # needing to create a window. This can be handy when you wan

Re: [Freesurfer] Merging aparc+aseg and ThalamicNuclei

As far as I can tell, mergeseg is in 7.4.1. Do you not see it in $FREESURFER/bin/mergeseg ? On 11/27/2024 5:30 PM, Andrew M wrote: External Email - Use Caution I'm looking to merge the aparc+aseg.mgz with outputs from additional seg steps such as  ThalamicNuclei (e.g., ThalamicNucl

Re: [Freesurfer] Pipeline for Transferring VBM Outputs to FreeSurfer and Parcellating with the Destrieux Atlas

I cannot tell from your description what you are trying to do. Can you elaborate? On 11/27/2024 10:44 AM, Safari, Nooshin (rvz7wf) wrote: External Email - Use Caution Hi experts, I am working on transferring VBM output, which is in NIfTI format, to FreeSurfer space. I would like to

Re: [Freesurfer] FDG Pet: How do I create an 'SUVR Image'?

Can you send the log file and the gtm.stats file? The command you have should rescale based upon the intensity in cerebellum gm and wm. Have you looked at your FDG volume to make sure it looks ok in cblum? On 11/26/2024 10:15 PM, Lai, Ian M. wrote: External Email - Use Caution I am

Re: [Freesurfer] Recon-all failing

Not sure what is going on. The log file uses 7.3.2, not 7.2.0, at least on the last invocation. Also, it does not indicate an error on the last call. If you are running it on a previously existing folder, maybe a file is there but corrupted. On 11/26/2024 5:33 PM, Mark Wagshul wrote:   

Re: [Freesurfer] mri_coreg threads parallel processing clarification

It looks like it is only using one thread, though you have correctly specified 10. I often run it with more than 1, and it certainly uses as many as I give it. It is possible that it is not allowed to have that many threads. Have you been able to run other programs with multiple threads? You ca

Re: [Freesurfer] FS version 8-beta

nning on Ubuntu 24. > > recon-all -all -s sub_fs -i ./sub/mri/orig/001.nii.gz -T2 > ./sub/mri/orig/T2raw.nii.gz > > Thanks, > > Martin > > On Thu, Nov 7, 2024 at 6:54 PM Douglas N. Greve > wrote: >> Hi All, as some of you have figured out, we have a beta versi

Re: [Freesurfer] update from 7.1 to 7.4

You can use the new version. It will only change the output if you change the options. On 11/22/2024 5:07 PM, Eszter Boros wrote: External Email - Use Caution Dear FreeSurfer Team, We did a longitudinal analysis with Freesufer 7.1.1 (two-stage longitudinal model) 2 years ago, and no

Re: [Freesurfer] mri_glmfit error：ill-conditioned matrix

FemaleNP only has two members but you are trying to fit 3 parameters (offset, AgeM slope, meanthickness slope). You need to have at least 3 members to do this, and you'll probably want much more. On 10/21/2024 2:37 PM, Chen Yang wrote: > External Email - Use Caution > > Dear FreeSurfer

Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples

ls. Thanks! Hansol *From: *freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Date: *Tuesday, November 12, 2024 at 10:55 AM *To: *freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples what is your comma

Re: [Freesurfer] Help with mri_vol2surf incorrect surface generation

your command line looks right. Try using the .lta file created by bbregister instead of the .dat file On 11/15/2024 10:34 AM, Pandey, Shraddha wrote: External Email - Use Caution We are experiencing issues with `mri_vol2surf` generating an incorrect surface for the `Paramagnetic.nii

Re: [Freesurfer] mri_coreg error: could not open brainmask.mgz file to register PET image with anatomical

Does /apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz, exist? Usually people are not putting their subjects in the FS subjects folder, so I'm wondering if your SUBJECTS_DIR is set correctly.

Re: [Freesurfer] use and registration of FLAIR in recon-all and segmentHA (@Eugenio)

On 11/12/2024 6:58 AM, Simone Cauzzo wrote: External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registe

Re: [Freesurfer] Resampling FLAIR images with anisotropic voxels

Is this just a visualization issue? What is your freeview command? On 11/12/2024 3:55 AM, Koen Van Leemput wrote: External Email - Use Caution Hi Jin, To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for

Re: [Freesurfer] Appropriate image for texture/intensity based analysis

I would recommend the norm.mgz as it should be scaled so that the WM is 110 and bias fields would have been (mostly) removed. On 11/12/2024 12:06 AM, Sandhitsu Das wrote: External Email - Use Caution We want to perform appearance-based analysis that also takes advantage of automated

Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples

what is your command line? On 11/11/2024 3:47 PM, Lee, Hansol wrote: Dear FreeSurfer developers, I am attempting to use “mri_vol2surf” command to project output from diffusion MRI models (e.g., DTI) onto the cortical surface. The registration between the diffusion MRI and anatomical space

Re: [Freesurfer] mri_label2label

Can you take a look at your images and the aseg.presurf.mgz segmentation and the rh.orig.nofix? The program that is throwing an error is trying to determine where the non-cortical medial wall is based on the aseg and the orig.nofix. If one or both of those are bad, then it may fail. On 11/11/

Re: [Freesurfer] aparcstats2table & asegstats2table version differences

It is certainly fixed in 7x version. I think it is fixed in the patch per the documentation On 11/7/2024 3:41 PM, Heffernan, Zachary wrote: External Email - Use Caution Hello FreeSurfer Mailing List, I see in the Release Notes

Re: [Freesurfer] FS version 8-beta

FreeSurfer? On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve wrote: Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns. The release notes are here *MailScanner has detected a

[Freesurfer] FS 8-beta bug report

FYI: I just found a bug where recon-all will exit with error the second time it is run. This will be fixed in the final release. doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

Re: [Freesurfer] PVC on DCE MRI

On 10/25/2024 2:00 PM, Shen, Qian wrote: External Email - Use Caution Hi FreeSurfer Team, We are looking to apply voxelwise PVC on our dynamic contrast-enhanced (DCE) MRI data using methods implemented in PETSurfer. Our DCE MRI data voxelsize =1x1x5mm, and we have used the Patlak m

Re: [Freesurfer] mri_glmfit-sim Error for Custom Threshold

You will need to add  --mczsim-dir /path/to/your/tables Or copy your tables into $FREESURFER/average/mult-comp-cor/fsaverage On 10/25/2024 1:20 PM, Sujeevini Sujanthan wrote: External Email - Use Caution Dear Freesurfer Experts, I'm encountering an error when attempting to run mri_gl

Re: [Freesurfer] glmfit-sim question

This is counter-intuitive but reasonable and expected. The distribution of cluster sizes changes as you change the CFT. When you raise the CFT, clusters get smaller, but the clusters under the null also get smaller  too. It may be that the smaller cluster size is actually less likely under the

[Freesurfer] FS version 8-beta

Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns. The release notes are here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes which I have copied below. One bug that we have already fo

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, September 30, 2024 17:02 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta

Re: [Freesurfer] petsurfer using brainstem subfields

default even when other PVC and tfe is turned off? Correct. I think it may just be rescaled. You can use mueller-gartner (--mgx) to voxel-wise pvc of GM Regards, Sneha *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, September 20, 2024 9:36 AM *To

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

Use mri_coreg --mat2par file.lta On 9/29/2024 5:48 AM, noga.ker...@campus.technion.ac.il wrote: External Email - Use Caution Hello FreeSurfer Developers, I am using |mri_robust_register| to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a

Re: [Freesurfer] morphometry protocol - cross site/platform?

You can check out ADNI, though they have made protocols on all machines based on the minimal protocol for the lowest performing scanner, so you may take a hit in overall performance. On 9/26/2024 5:35 PM, Mira Michelle Raman wrote: External Email - Use Caution Good afternoon,  I was

Re: [Freesurfer] Questions re Freesurfer editing

I'm not sure what to do about the medial surfaces. I don't think I've run into that problem before. For the other issue, those areas are the transverse sinus veins. In the next version, I have something that will segment those areas. You can get it now in the dev version. Then run mri_vsinus_se

Re: [Freesurfer] Hippocampal segmentation on two sets of MRI with different resolution

I don't  know, probably an open question. The change in resolution will certainly affect results. Using the higher res (ie, not downsampling to 1mm) will likely give you the best result. On 9/19/2024 10:38 PM, Jacob Bunyamin wrote: External Email - Use Caution Good afternoon, I have

Re: [Freesurfer] petsurfer using brainstem subfields

It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_

Re: [Freesurfer] Question on lateral ventricle segmentation

No, there is not an easy way to break it up that way. If you know some programming, you could merge all 3 into one seg, then compute the PCA of the coordinates, then divide it up along the largest direction On 9/9/2024 1:54 AM, Necati Emre Şahin wrote: External Email - Use Caution De

Re: [Freesurfer] (no subject)

Does it run with the --cpu flag? That will run it with the cpu and thus isolate your problem to the gpu/cuda On 9/9/2024 10:31 PM, Matthew Lynch wrote: External Email - Use Caution I run this command: mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test an

Re: [Freesurfer] Error in dt_recon

The argument to the --s flag should be the name of the subject as was specified when you ran recon-all, eg recon-all -i t1_SPGR.nii  -s subjectname -all Then use dt_rcon -s subjectname ... On 9/12/2024 7:45 AM, Ramesh Babu wrote: External Email - Use Caution Dear All, I am new to dti

Re: [Freesurfer] Longitudinal base processing error

that could certainly be a problem. Is it really just a single value throughout the brain? If so, that is the problem. On the other hand, it could be that the freeview intensity limits are not set well, so try playing with those. You can also click on voxels in the brain and look at the values i

Re: [Freesurfer] Recon-all -all for many MRI sequences?

you have to pass it the file(s) you want to analyze. If you have a bunch of dicoms, and your T1 is just one of many, you have to figure out one of the files that corresponds to the T1. Or you can use dcmunpack, eg, dcmunpack -src /path/to/your/dicoms -targ outputfolder -auto-runseq mgz That comm

Re: [Freesurfer] petsurfer questions - No PVC stats file in the similar format as gtm.stats.dat

looks like it is only different in the first or second decimal place, is that right? If so, then it is acceptable. On 8/22/2024 4:11 PM, Sneha Pandya wrote: External Email - Use Caution Dear team, A] I am running mri_gtmpvc on our data and need to extract stats data that is in the s

Re: [Freesurfer] PetSurfer: PET SUVR analysis

On 8/13/2024 12:38 AM, WONG Wan Wa wrote: External Email - Use Caution Hi FS experts, I want to do PET SUVR analysis using PetSurfer. When determining the FWHM of the PSF of the scanner, is it the same value for Siemens (Biograph40_mCT vs. Biograph128_mCT) or (Biograph64_Vision 600

Re: [Freesurfer] How to change mri_convert --conform to use another flag while running recon-all

You can add -cubic to the recon-all command line (though you might get cubic at other times, but that probably won't hurt) On 8/19/2024 1:40 PM, Jeiran Choupan wrote: External Email - Use Caution Dear Freesurfer support team, I noticed that the interpolation setting used within the f

Re: [Freesurfer] PetSurfer: how to convert nopvc.nii.gz to a format like gtm.stats.dat?

You can run something like mri_convert nopvc.nii.gz --ascii nopvc.dat This will give you a text file To put a bunch together across subject, you can run something like mri_concat */nopvc.nii.gz --o all.nopvc.nii.gz Then do the same trick as above. On 8/20/2024 12:01 AM, WONG Wan Wa wrote:

Re: [Freesurfer] Question: Recon-all Using T1/T2 Mutual Information

I'm not sure what you mean. Usually, one would edit the proper volumes in freeview using the protocol described (eg, setting edited voxels to certain values). One can implement automatic edits as long as one keeps to the protocol. On 7/30/2024 5:09 PM, Edwards, Vincent wrote: Externa

Re: [Freesurfer] FreeSurfer in fmriprep

ow if more information is needed!  Thanks so much! Best, Tengwen *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, July 29, 2024 12:26 PM *To:* freesurfer@nmr.mgh.harvard.edu *Su

Re: [Freesurfer] FreeSurfer Question

please send your command line, terminal output, and stats file On 7/23/2024 3:07 PM, Selena Gangaram wrote: External Email - Use Caution Hi, I hope you are doing well, I subscribed to your mailing list to ask my question! I was wondering if you knew the reason as to why my extracti

Re: [Freesurfer] FreeSurfer in fmriprep

please send the recon-all.log file in the scripts folder On 7/23/2024 2:14 PM, Tengwen Fan wrote: External Email - Use Caution Dear FreeSurfer Developers, I hope this email finds you well! I am using fMRIprep to do pre-processing. The fMRIprep combines methodology from AFNI, ANTs, F

Re: [Freesurfer] Scalp mask

You can try mri_seghead and/or mideface (which uses mri_seghead) On 7/16/2024 6:27 AM, Francesco Lomi wrote: External Email - Use Caution Hi everybody, Do you know how to create a scalp mask file with freesurfer? Thank you in advance Francesco ___

Re: [Freesurfer] Longitudinal analyses using Repeated measures anova

Sorry, there is nothing here (ie, no fsgd file, no images). Did you mean to attached? On 7/10/2024 5:31 AM, Josefine Tingdal Taube Danielsen wrote: External Email - Use Caution Hi Freesurfer support, I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64. freesurfer-linux-ubuntu22_

Re: [Freesurfer] Negative voxel ranges

in FS, all the voxel indices are >= 0 I don't know what the numbers mean you put below On 7/15/2024 6:35 AM, ERNEST KISSI wrote: External Email - Use Caution Dear fresurfer team, Please I want to extract the intensity of a voxel  48, -56, -34. But my voxel ranges of my image does not

Re: [Freesurfer] Very large segmentation errors with recon-all

m that occurred. Best, Danilo *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Sunday, July 14, 2024 4:56:22 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesur

Re: [Freesurfer] Maps from fsLR system (32, 492 vertices) to fsaverage5

You'll have to create curvature files, inflate the surface to a sphere, then run mris_register On 7/10/2024 10:10 AM, Stefano Delli Pizzi wrote: > External Email - Use Caution > > Dear, > > We are using the Magicc Maps (https://github.com/kwagstyl/MAGICC). The maps > are in fsLR system

Re: [Freesurfer] Very large segmentation errors with recon-all

what you are showing there is not a segmentation error but a severe misalignment. What is your freeview command line? Are you sure that the anatomicals and the surfaces are from the same subject? On 7/10/2024 4:59 AM, Tornabene, Danilo wrote: External Email - Use Caution Dear FreeSur

Re: [Freesurfer] Functional connectivity: sig.nii.gz values seem off

Have you looked at the individual subjects? This will sometimes happen when there are strong global signals as the global signal (by definition) gets into the regressor and is everywhere, so you end up with these large swaths of positive activation. You're already doing the things I would sugge

Re: [Freesurfer] Doing math on mgz file

you can also use fscalc, which is a frontend for mris_calc On 7/9/2024 3:14 PM, Aaron Tanenbaum wrote: External Email - Use Caution Perfect thank you On Tue, Jul 9, 2024 at 1:30 PM Huang, Yujing wrote: Is this what you are looking for? https://surfer.nmr.mgh.harvard.edu/p

Re: [Freesurfer] Licence for using Freesurfer-generated images in a book?

I think you can use any picture you want without permission. On 7/8/2024 7:14 AM, ALARIO Francois wrote: External Email - Use Caution Hello I am considering using freesurfer-generated images not in a scientific paper but in a popular science book (commercial). What is the preferred

Re: [Freesurfer] mri_gtmpvc RBV - cannot find file from a custom subject directory

That is the way I would have suggested. Does it run to completion when you use the softlink? Reorganizing the folder structure it likely to break a lot of things. On 7/11/2024 10:02 AM, Sneha Pandya wrote: External Email - Use Caution Dear team, I am running mri_gtmpvc using RBV cor

Re: [Freesurfer] Robustness of Segmentation and Parcellation to Lesions

On 7/3/2024 7:19 PM, Hickman, Leonard B. MD wrote: External Email - Use Caution Hello all, I am using FreeSurfer to measure specific cortical parcellations and subcortical segmentations in a medium-sized dataset (over 150 scans). About a fifth of the scans include cortical lesions

Re: [Freesurfer] data in folder 'stats'

It is not normalized. these are volumes, surface ares, and thicknesses of various regions. I'm not sure what common space corrections you could do. You can correct for eTIV On 7/3/2024 1:11 PM, PATRICIO FELIPE RIQUELME wrote: External Email - Use Caution Hi everyone. I just began to

Re: [Freesurfer] Scanner and Freesurfer-version differences

On 7/1/2024 1:05 AM, Bronwyn Overs wrote: External Email - Use Caution Hi Freesurfer Mailing List, I work on a large bipolar disorder imaging study that has been running for over 10 years. We previously acquired 2 sMRI time-points (pre 2013, /n/~500, /n/~250 at each time-point) on

Re: [Freesurfer] Inquiry about alpha inflation in multiple comparison

Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 6/28/2024 9:48 AM, Emma Harper wrote: External Email - Use Caution Dear Freesufer teams, Does anyone have any recommendations to correct for alpha inflation when doing the mul

Re: [Freesurfer] FreeSurfer atlases

have suggestions? Thanks, Alice *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, June 27, 2024 12:36 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer atlases I'm not sure wha

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