Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

Can you run it with -debug as the first option, capture the output, and send it to me? It will be a lot of output, so just capture it in a file and send the file, eg preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force | tee pps.log

Re: [Freesurfer] FW: Create a Binarized ROI for Surface

is? Thank you so much! Regards, Xiaoxu *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, January 19, 2024 3:16 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FW: Create a Binarized ROI for Surface On 1/19/2024 3: 45 PM, Na, Xiaoxu

Re: [Freesurfer] FW: Create a Binarized ROI for Surface

On 1/19/2024 3:45 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear Freesurfer Expert, While the sphere can only be drawn using that Dr. Doug  suggested, the sphere option would mess up. Do you need help with this? If so, can you give more info? I have a further question

Re: [Freesurfer] Issue with mri_glmfit-sim

M, O'Neill, Alexandra Grace wrote: Hi Doug, Thanks so much for getting back to me. Below is our previous correspondence: *From: *freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Date: *Friday, January 12, 2024 at 4:19 PM *To: *freesurfer@nmr.mgh.harvard.edu *Su

Re: [Freesurfer] Issue with mri_glmfit-sim

Sorry, I already forgot  what the problem was. Can you include our previous correspondence? Also, make sure to reply to the list. Thanks! On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote: Hi Doug, Thank you for getting back to me. Unfortunately, the issue is persisting, and the command

Re: [Freesurfer] Applying Wang Atlas to Group Analysis Results in FreeSurfer

what is the wang atlas? volume or surface? On 1/19/2024 12:20 AM, Sujeevini Sujanthan wrote: External Email - Use Caution Hi, I would like to apply the wang atlas over the group activation maps produced from Freesurfer analysis. I would appreciate any guidance/instructions you can

Re: [Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

That does not look like it is a problem with the input image. Do you have a normal, invivo MRI that you can run samseg on to see if it is just a problem with your platform? On 1/18/2024 3:57 AM, K Eswar wrote: External Email - Use Caution Dear FS community I have an ex-vivo human

Re: [Freesurfer] T1map processing error

The way I have done this was do compute T1w images (MPRAGE) through simulations, then run recon-all on that. On 1/17/2024 11:55 AM, Maksim Slivka wrote: External Email - Use Caution Dear FS community, Recently our lab started collecting 3D-QALAS (Cho et al., 2023). Using this

Re: [Freesurfer] Sample registration question

if this would require a voxel wise analysis or an ROI analysis… to my understanding this is more of a ROI analysis between subjects - is this assumption incorrect? Thank you, Peter On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve wrote: So this is where I get confused on your intentions because

Re: [Freesurfer] Midline white/pial surface

I would also be helpful to have some pics of what you are seeing. The surface is not valid in the "medial well" -- ie all the non-cortical structures on the central sagittial plane such as thalamus an VDC. On 1/16/2024 7:50 AM, Huang, Yujing wrote: Can you try the troubleshooting methods

Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Friday, January 12, 2024 4:26 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] extracting measurements for mean gray matter thickness/LGI I don't understand. Why not use the mean thickness from FS? We have an lGI module

Re: [Freesurfer] Sample registration question

, Sorry I should have clarified. Yes, I would like to perform voxelwise analysis of FA and MD values of hippocampal subfield between subjects. Is this possible with free surfer? Thank you again for your time. M On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve wrote: oh, I thought you

Re: [Freesurfer] Registration of MPF to FLASH 3D image

, Jan 13, 2024, 12:31 AM Douglas N. Greve wrote: That is the bbregister command. You should look at the output of recon-all On 1/11/2024 5:37 PM, ERNEST KISSI wrote: External Email - Use Caution This what the output shows doing the bbregister. image.png

Re: [Freesurfer] Sample registration question

for each subject onto the same space for inter subject analysis of FA values? Thanks again, M On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve wrote: Map the diffusion data to the subfield space, eg, mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o fa

Re: [Freesurfer] Sample registration question

Choi wrote: External Email - Use Caution Hi there, Is there a way to successfully obtain FA/MD values from the hippocampus subfields? Thank you, M On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve wrote: I'm not sure what you mean. The subfields are an ROI-based analysis

Re: [Freesurfer] Including superficial white matter in cortical parcellation

I suspect the problem is with the aseg.mgz input. You can regenerate that with the new surfs with a different call to mri_surf2volseg. However, that will take a --fix-presurf-with-ribbon argument, so you will also have to regenerate the ribbon.mgz file for the new surfaces with mris_volmask

Re: [Freesurfer] poor inferior cerebellum segmentation

You can try using mri_synthseg --i orig.mgz --o synthseg.mgz it generally does a better job on cerebellum than the native FS command On 1/5/2024 4:11 PM, Carlos Alcocer wrote: External Email - Use Caution Hello, Inferior portion of cerebellum are not segmented well. It is included

Re: [Freesurfer] extracting measurements for mean gray matter thickness/LGI

I don't understand. Why not use the mean thickness from FS? We have an lGI module; we have not supported it in years, but maybe it still works. https://surfer.nmr.mgh.harvard.edu/fswiki/LGI On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use

Re: [Freesurfer] Sample registration question

I'm not sure what you mean. The subfields are an ROI-based analysis. Are you saying you want to do a voxel-based analysis (without reference to ROIs)? On 1/9/2024 12:05 PM, Mirsol Choi wrote: External Email - Use Caution Hi there Freesurfer, I am currently using freesurfer to take

Re: [Freesurfer] Issue with mri_glmfit-sim

I think v6 might be broken when using -bg. Try removing that. On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote: *Hello FS community,* * To correct for multiple comparisons for the results of a parametric modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer version 6.0 with

Re: [Freesurfer] Tksurfer and freeview

please send the command line and the terminal output. Also, try using tksurferfv (this is a wrapper around freeview that takes tksurfer-like commands) On 1/6/2024 8:59 PM, JAEHYUN KIM wrote: External Email - Use Caution Hello, I attempted to switch tksurfer to freeview in the

Re: [Freesurfer] modify intensity normalization pipeline

You can put control points in the temporal lobe. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview/ On 1/5/2024 4:24 PM, Carlos Alcocer wrote: External Email - Use Caution Hello, Is there a way to modify intensity normalization pipeline in recon-all

Re: [Freesurfer] Freesurfer Digest, Vol 239, Issue 1

: "Douglas N. Greve" mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: Boundary based registration To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: mailto:e31f2342-e539-4ecc-b146-2b059dab1...@mgh.harvard.edu>> Content-Type: text/p

Re: [Freesurfer] FLAIR vs. T1 question

The FLAIR is only used to place the pial surfaces. If you are interested only in WM, then it is not necessary. On 1/3/2024 3:35 PM, aliyas...@yahoo.com wrote: External Email - Use Caution Dear FS mailing list, My apologies if this is a naive question. I have FLAIR images that were

[Freesurfer] Bug in FSFAST functional connectivity analysis

There is a bug in the FSFAST functional connectivity seed-based analysis (current version and all previous versions). The amplitude of the seed waveforms are not rescaled in any way. This can affect the amplitude of the regression

Re: [Freesurfer] Manual/reproduce conform

If you want to keep the original orientation, you can specify --conform-dc. Would that fix your problem? On 12/21/2023 9:30 AM, Dipterix Wang wrote: External Email - Use Caution Dear FreeSurer Wizards, I'm trying to run the recon-all command on one of my template brains such that

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

Yes, that is correct On 12/20/2023 2:07 PM, Edwards, Vincent wrote: External Email - Use Caution Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer

Re: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w MR Images

btw, you can get fornix segmentation from mri_sclimbic_seg On 12/15/2023 11:34 AM, Huang, Yujing wrote: Can you try ‘mri_segstats’? It will compute statistics on segmented volumes  - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats Yujing *From:* Ahsan Ali *Sent:* Friday, December

Re: [Freesurfer] Case-controls study !

Try using DOSS (--fsgd your.fsgd doss) instead of DODS (which is the default). On 12/8/2023 12:03 PM, Martin Juneja wrote: External Email - Use Caution Hello FreeSurfer experts, In my case-control study, I have a dataset of 5 healthy controls (HCs) and one patient (PAT). I was

Re: [Freesurfer] Create a Binarized ROI for Surface

I think that will work, but there are better tools for this kind of thing. If you have 7.4, you can use mri_binarize, like mri_binarize -dilate-vertex vno surf radius outmask where vno is the center vertex, surf is the surface (eg, white), radius is the desired radius of the cicrle, and outmask

Re: [Freesurfer] mri_cc question

On 12/13/2023 7:47 AM, Dawn Matthews wrote: External Email - Use Caution Hello Freesurfer team and thank you for your continued responses to questions.  My questions pertain to mri_cc, and subsegmentation of the corpus callosum.  In prior runs of version 6.0, it seems that aseg

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

Yes, that is correct. On 12/13/2023 3:01 AM, Edwards, Vincent wrote: External Email - Use Caution Hello, I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be

Re: [Freesurfer] FW: Boundary based registration

Have you tried using the "intermediate" option (--int) in bbregister? The intermediate volume should be a whole brain volume and it should share a RAS space with the slab volume (eg, if they were acquired in the same session; load both the slab and the intermediate in freeview to see if they

Re: [Freesurfer] Use pial or white surface area of FreeSurfer?

We usually use the white surface because its placement is independent of the placement of the pial surface (and so independent of thickness and volume), but it is really an empirical question. On 12/12/2023 11:26 PM, free_learner wrote: External Email - Use Caution Dear experts,

Re: [Freesurfer] Tksurfer option for horizontal scale bar

tksurfer was deprecated years ago, though it's replacement (freeview) does not seem to have that capability either. On 12/12/2023 2:29 PM, Lee, Jeungchan wrote: Hi Freesurfers, I’m using TkSurfer to visualize my results and want to add a horizontal color scale bar. I used [

Re: [Freesurfer] Brainnetome atlas

I have not worked with the Brainnetome atlas so I don't know what it will take. Maybe talk to the Brainnetome developers? On 12/12/2023 11:05 AM, Blanca Zufiria Gerbolés wrote: External Email - Use Caution Dear all, I would like to extract the cortical thickness, subcortical volumes

Re: [Freesurfer] Help with transform matrix for SEEG

Have you seen this page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ? On 12/10/2023 8:55 AM, Hyunchul Lee wrote: External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have

Re: [Freesurfer] Clear background from command line

Not sure what you mean by the background. You can try binarizing the electrodes (mri_binarize), then load it as a segmentation. On 12/8/2023 5:47 PM, Datta, Aditya wrote: External Email - Use Caution Hi, Is there any way to clear background for a volume file from the command line.

Re: [Freesurfer] MEMPRAGE dura flags

sorry, what is the dura flag you are talking about? Also, dura generally interferes with the placement of the pial surface, not the white (ie, white-gray boundary) surface. On 12/7/2023 2:20 PM, Akkoyunlu, Beyza wrote: External Email - Use Caution Hi, I have longitudinal data with

Re: [Freesurfer] Cortical Thickness Measurement in Cortical Lesion ROI

You should load $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz into freeview with the surfaces, eg cd subject/mri freeview nu.mgz $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz -f ../surfs/?h.white ../surfs/?h.pial and see if the lesion maps between the white and

Re: [Freesurfer] Correlation Line Plot for FS Group Analysis

No, sorry, that was only available in the old tksurfer/tkmedit. We have not implemented it in freeview. On 12/6/2023 6:37 PM, Tejaswi D. Sudhakar wrote: External Email - Use Caution Hello, I am to generate a plot to visualize the slopes between classes for group analysis. I would

Re: [Freesurfer] Longitudinal pipeline with multiple scans at one time point

You are right that using all the scans will bias toward tp2. I think I would just run the cross for each time point using all the data you have. This will not bias the base because an average of the images within each time point will be used to make the base. If possible, you will want to make

Re: [Freesurfer] volumetric to surface using mri_vol2surf: tpl-MNI152NLin2009cAsym

What volume and what surface? You can recon-all the MNI152NLIN2009cAsym to generate surfaces, then they will be in registration directly On 12/6/2023 10:30 AM, Lee, Jeungchan wrote: Hi Freesurfers, I was wondering if there is a registration matrix (from volumetric to surface) for

Re: [Freesurfer] PETSurfer

Hi, sorry for the many months to get back to you. I have just updated the documentation on https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer to indicate how to use your own segmentations. I'm assuming that you have a volume with choroid plexus labeled that you want  to merge into the stream.

Re: [Freesurfer] Saving more than one label in a single volume file

sorry, not sure what you mean. do you mean you want to extract, say, two labels (amygdala and hippocampus) into a single volume file? If so, you can run something like mri_binarize --i aseg.mgz --match 17 18 --o amyg-hippo.lh.mask.mgz mri_mask aseg.mgz amyg-hippo.lh.mask.mgz amyg-hippo.lh.mgz

Re: [Freesurfer] Calculating LGI with existing masks

sorry, not possible On 11/29/2023 1:59 PM, Ding, Yan wrote: External Email - Use Caution Hi, I am new to FreeSurfer. And I have a question regarding the calculation of the local gyrification index (LGI). I have one brain MRI image and I have manually created the mask of the

Re: [Freesurfer] Group Analysis - 4 groups 3 covariates

On 11/29/2023 2:16 PM, Tejaswi D. Sudhakar wrote: External Email - Use Caution Hi, I would like to run a group analysis on 4 groups (patientM, patientF, controlM, controlF) with 3 covariates (age, cogscore1, cogscore2). I am running with dods - so I would have 16 total

Re: [Freesurfer] Cannot locate reg.lta

You have to create your own registration. Eg, try bbregister On 11/28/2023 6:42 PM, Mirsol Choi wrote: External Email - Use Caution Hi there, I am currently trying to run vol2subfield command that allows us to get a registration between an input volume (ie. FA map) to a subfield

Re: [Freesurfer] issue with mri_vol2surf

2023-11-22 at 1.32.53 PM.png  doesn't allow me to adjust the threshold to negative values, for example t-values between -3 and 3. On Wed, Nov 22, 2023 at 1:26 PM Douglas N. Greve wrote: Have you tried adjusting the threshold. Open the configure overlay option. Also, sending a pic would

Re: [Freesurfer] Reopen issue 898: mri_binarize --replace misbehavior

Nick, what happens if you reverse the order (ie, do 15 72 first, then 11 15)? On 11/28/2023 12:27 PM, Nick Schmansky wrote: External Email - Use Caution I have encountered the problem that chrisadamsonmcri

Re: [Freesurfer] xhemi

Yes, they are. BTW, you should not need to mri_convert the thickness to mgh format On 11/27/2023 10:01 AM, Joost Janssen wrote: External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The

Re: [Freesurfer] Fwd: Errors in LGI command

Copy the attached matlab file into $FREESURFER/matlab/freesurfer_read_surf.m On 11/24/2023 12:53 PM, 笹林大樹 wrote: External Email - Use Caution Dear Freesurfer experts, I’m sorry, I would like to add some missing information about the following question. OS: CentOS Linux 7 FS ver:

Re: [Freesurfer] Functional data analysis with longitudinal data

Is the fmri also longitudinal? If so, register to the closest time point On 11/26/2023 5:53 AM, Akkoyunlu, Beyza wrote: External Email - Use Caution Hi, I am doing a longitudinal experiment and I already run the longitudinal anatomical pipeline. I am not sure which anatomical data

Re: [Freesurfer] Freesurfer's Matrice for reading a nifti Image

Try this https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 11/26/2023 9:17 AM, Yazdan Rezaee Jouryabi wrote: External Email - Use Caution Dear all, Hi I'm looking for the convention of freesurfer which is used for reading a nifti Image, as we are familiar with a nifti

Re: [Freesurfer] Extracting Beta Values from FSFAST

The first 5 will be the condition betas averaged across all runs. The other 28 are 4 skips * 4 runs = 16 3 polyfit (0,1,2) * 4 runs = 12 On 11/24/2023 11:14 AM, Deyan Mitev wrote: External Email - Use Caution Hello Freesurfer Developers, I want to extract the beta values for an

Re: [Freesurfer] Transformation of volume images

. Best regards, Peter On Wed, Nov 22, 2023 at 7:09 PM Douglas N. Greve wrote: You can use  something like mri_convert orig.mgz -at mri/talairach.m3z orig-in-mni305.mgz This is nonlinear. It takes you to the mni305 space. On 11/21/2023 11:45 AM, P Pieperhoff wrote:

Re: [Freesurfer] No ROI name in summary of MNI305 group analysis

Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat On 11/23/2023 2:32 AM, wangzhiwei3233 wrote: External Email - Use Caution Dear Freesurfer Experts, I did group-level analysis in MNI305 space.  Then I output the summay via command 'mri_volcluster' as follows:

Re: [Freesurfer] issue with mri_vol2surf

Have you tried adjusting the threshold. Open the configure overlay option. Also, sending a pic would be helpful (and the contents of tk.dat) On 11/22/2023 11:29 AM, Atena Akbari wrote: External Email - Use Caution Dear freesurfer team, I want to overlay the activation map that I got

Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

/MRS_101_coregistration.lta --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistered.mgz Kind regards, Jeltje Spapens *From: * on behalf of "Douglas N. Greve" *Reply to: *Freesurfer support list *Date: *Tuesday, 21 November 2023 at 18.31 *To: *"freesurfer@nmr.

Re: [Freesurfer] recon-all error - MRISlabel2Mask()

yes, sending the full log file will be helpful. My guess is that the surfaces got out of synch (eg, if you had done edits). On 11/21/2023 8:15 PM, Mark Wagshul wrote: External Email - Use Caution Dear Freesurfer experts, Hi. Hoping someone can give me some guidance in how to proceed

Re: [Freesurfer] Distance Measurement After recon-all

You can use mri_vol2surf, something like mri_vol2surf --closest-vertex x y z coords ltafile surf outfile where xyz is a coordinate (eg, the center or edge or you lesion). coords: 1=scanner,2=tkreg (you can pick the xyz from the freeview scanner or tkreg ras) if these coordinates are in the same

Re: [Freesurfer] Transformation of volume images

You can use  something like mri_convert orig.mgz -at mri/talairach.m3z orig-in-mni305.mgz This is nonlinear. It takes you to the mni305 space. On 11/21/2023 11:45 AM, P Pieperhoff wrote: External Email - Use Caution Hi Yujing, thank you for your help! But I think, this is only the

Re: [Freesurfer] Fwd: About Mean LGI value

lated here). Are these values acceptable? Daiki Sasabayashi 2023/11/09 9:33、Douglas N. Greve のメール: How different are the values? Those two stats files are created with different programs, so there could be some small differences. But if you're seeing large differences, then that is some

Re: [Freesurfer] total intracranial volume

They are not On 11/20/2023 6:01 AM, yunus soleymani wrote: External Email - Use Caution Hi Freesurfers, I wanted to know if the Freesurfer volume results are already normalized by the total intracranial volume or if I should normalize it for each subject myself. Thanks for your

Re: [Freesurfer] run recon-all with already skull-stripped data

did you look at the results (eg, the aseg)? Can you send the recon-all.log file? On 11/19/2023 11:18 PM, June Kang wrote: External Email - Use Caution Hello, According to the FAQ for earlier version of Freesurfer (maybe 6.x), the instruction is below. First you must run only

Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

Do you see the same thing in the source BA data (in fsaverage)? On 11/21/2023 10:22 AM, Marawi, Tulip wrote: External Email - Use Caution Dear FreeSurfer developers, Our research group used the FreeSurfer’s recon-all tool to reconstruct 74 anatomical images from cognitively healthy

Re: [Freesurfer] Doubts about GLM contrasts

University of Rio Grande do Sul - Porto Alegre/RS - Brazil - Douglas N. Greve <https://secure-web.cisco.com/1yYgRLzmOCtuh8UFLaxt4ucohab6Ii9cqIDNXc9_tUgQITTp1lOWVlAhzXYGkoInMWkZJnqBum7Q2bchzciGSB2Na5ppT64MdUHXfn7DI7OxVbl4tT_fQgG0kh4IlbeSX880ZgCJICom9qj1NBstIOI_qjcTChjX

Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

Is MRS_201_MT_tfl_stripped.mgz  correctly oriented when you view it in freeview? Also, bbr is meant to be used for within subject registration. For something like registering to the mni152, try mri_coreg and specify --dof 12 On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote:

Re: [Freesurfer] recon-all error

And how  did you create 001.mgz? Sometimes SPM will put NaNs in the image to indicate a mask. On 11/17/2023 10:12 AM, Huang, Yujing wrote: Hi Carlos, Can you attach recon-all.log? Best, Yujing *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Carlos Alcocer *Sent:*

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

)  as such: << echo “1 -1” > File_Name.mtx and have never had issues, however I have not used "[ ] " on my contrasts before... Thank you so so much for your willingness to help and your time! On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve wrote: Can you send /data/

Re: [Freesurfer] Question about lesions output of samseg

Internally, samseg uses partial volume to compute a more accurate volume. They should still be very close though. On 11/16/2023 6:46 AM, reza razmara wrote: External Email - Use Caution Hi freesurfer team I use samseg for lesion segmentation. In the result of .stats i see the

Re: [Freesurfer] Problem with brainstem overlap after BBR

I answered it yesterday. Check your inbox On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote: External Email - Use Caution Hello Freesurfer Developers, I have never received an answer to my problem, maybe it was lost in the e-mails. Kind regards, Jeltje Spapens *From: *"Spapens,

Re: [Freesurfer] Create an lta or xfm file for mri_vol2vol

You have to know the coordinate system of the matrix. See, eg, here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems Once you know the coordinate system, I would use lta_convert to generate an appropriate file, eg, lta_convert --inlta identity.nofile --src preop.mgz   --trg postop.mgz 

Re: [Freesurfer] Mapping input volume (fa.nii) to hippocampus segmentation volume

Can you run it with --debug as the first option and send the resulting terminal output? On 11/9/2023 12:54 PM, Mirsol Choi wrote: External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

Caution Hi Douglas, Thank you for your reply. Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0 0]/3 As well as the code I am running and the whole output from the terminal. Thank you so much for your help! On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve wrote

Re: [Freesurfer] mri_cvs_register failure

You can map the curvature from fsaverage to the individual (or reverse) and then load both on the surface to see if they agree. I think that CVS will/can save intermediate registrations, so you might check those to see if the problem is cropping up at a particular step. On 11/9/2023 8:18 AM,

Re: [Freesurfer] Problem with brainstem overlap after BBR

Several things - don't use --init-fsl. If you don't specify, then it will use mri_coreg, which will work better. You can also try --init-header - your movable scan appears to be t2 weighted, so use --t2 instead of --t1 - look at the cost file (or send it). It is hard to say what the cost

Re: [Freesurfer] Doubts about GLM contrasts

Yes, that looks right (assuming that cortisol is your first variable) On 11/7/2023 3:49 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, Following the FSGD examples on the website, I built the following test: Question: Is there an

Re: [Freesurfer] ANTs denoising

ANTs denoising is not used by default. Ants N4 is used to crfeate nu.mgz On 11/6/2023 11:46 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution To which anatomical volume is ANTs denoising applied to for generating the orig surface? We do ANTS denoising to the input T1

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

Can you send the command line, all the terminal output, and your fsgd file? On 11/3/2023 11:51 AM, Ludmila Midrigan wrote: External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error:

Re: [Freesurfer] About Mean LGI value

26q%3Dsubject%3A%2522Re%255C%253A%2B%255C%255BFreesurfer%255C%255D%2BMean%2BGyrification%2Bindex%2522%26o%3Dnewest> Douglas N. Greve <https://secure-web.

Re: [Freesurfer] Group analysis question

So you are trying to predict the neuropsych battery from brain measurement? This is not how mri_glmfit is usually used, but it is just a GLM so it is possible. You'd have to set up a table for the --table input. You can try running asegstats2table to get an example table, then you'd just set

Re: [Freesurfer] dt_recon question

On 10/30/2023 9:50 PM, Mirsol Choi wrote: External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my

Re: [Freesurfer] SynthSEG continued developments

My experience is that it is extremely robust with respect to defacing (and even skull stripping). On 10/30/2023 12:02 PM, Iglesias Gonzalez, Juan E. wrote: Dear Dawn, Integrating the hippocampal subfields into SynthSeg in on the to-do list, but it’s tricky due to differences in resolution.

Re: [Freesurfer] PETsurfer kinetic modeling

There is not an easy way to do this yet. If you have your segmentations in the conformed anatomical space, you can merge them with gtmseg.mgz with something like mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o yoursegs-in-gtmseg-space.mgz mergeseg --src gtmseg.mgz --merge

Re: [Freesurfer] Loading surfaces

This usually means that you edited a recon, then reran recon-all but only partially leaving the surfaces out of sync. On 10/25/2023 11:40 AM, Huang, Yujing wrote: Hi Nicole, The error message indicated the number of vertices or the number of triangles don’t match in the two surface files it

Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual

fsxvfb is just a script that sets up an env for running Xvfb. I wrote this script and got it working, but I'm not an expert on Xvfb, so you'll have to figure it out yourself. You can try to running another program that brings up an image (eg, fsxvfb glxgears) to make sure it is not a freeview

Re: [Freesurfer] mri_cvs_register failure

I'm not sure what happened. Have you checked the surface-based registration? Also check the talairach reg. On 10/19/2023 11:35 AM, Antonín Škoch wrote: External Email - Use Caution Dear experts, I have encountered an failure of mri_cvs_register --mov my_subject --mni The resulting

Re: [Freesurfer] .lta vs .dat questions

Hi Corinna, the two files should give the same vol2vol output. Can you send your command lines and pics of how they are different? The fscale was only used by the old tkregister program to control the brightness. doug On 10/18/2023 1:44 PM, Corinna Bauer wrote: External Email - Use

Re: [Freesurfer] TR: Issues at the "tailarach_avi" transformation step of recon-all

The UNI scan will likely fail for the talairach. One thing you can try is -samseg-reg, which will compute the tal reg using samseg (which will be much more robust). However, it wont surprise me to see it fail somewhere else along the stream. On 10/18/2023 8:57 AM, Hensenne, Eva (Stud. FHML)

Re: [Freesurfer] Atrophy Maps on Coronal Slices

I'm not sure what you mean. Can you elaborate? On 10/17/2023 5:36 PM, Daniel Gutstein wrote: External Email - Use Caution Is there a methodology in FreeSurfer for creating atrophy maps and displaying them on individual coronal slices? Thank you. *Daniel Gutstein* Research Data

Re: [Freesurfer] Common space

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 10/17/2023 11:55 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions.

Re: [Freesurfer] Problem with mri_robust_register when using segmentThalamicNuclei.sh

This looks like an error inside of fmriprep to me. If you want our help, please recreate the error using just the FS tools On 10/11/2023 2:08 PM, Xingyu Liu wrote: External Email - Use Caution Dear freesurfer experts, I was trying to segment thalamic nuclei using 

Re: [Freesurfer] FSPGR Recon All Error

Not sure what is going wrong here. Try looking at the images and the initial segmentation, eg, freeview norm.mgz aseg.presurf.mgz Does anything look off? On 10/8/2023 11:05 AM, Massimo Valerio wrote: External Email - Use Caution Il giorno dom 8 ott 2023 alle ore 16:58 Massimo Valerio

Re: [Freesurfer] registration of a rescaled volume

Do you just need to change the voxel size for that dimension? If so, you can use mri_convert, something like mri_convert -iis newvoxsize input.mgz output.mgz where -iis means the change the voxel size of the first dimension. Use -ijs or -iks for the 2nd and 3rd. You may have to play with it to

Re: [Freesurfer] Project volumetric MTR data on surface

You are on the right track. First, you need a registration matrix. You can get this with bbregister --mov mtr.nii.gz --reg reg.lta --s subject --t2 The above command assumes that GM is brighter than WM in MTR. If this is not the case, then use --t1 View your registration with tkregisterfv --mov

Re: [Freesurfer] Possible Skull-Stripping Error in Many Subjects (FS7.2)

have you looked here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview ? On 10/4/2023 4:20 PM, Carly McIntyre-Wood wrote: External Email - Use Caution Hi there, I have recently been looking at the aseg.mgz file in several of the participants I have ran

Re: [Freesurfer] FSGD file and constrast

That is correct for DOSS (note that you don't need to do the pos and neg separately as you can handle that at the next stage; in the sig maps, the pos will show up as red/yellow and neg will show up as blue). For DODS you would need 0 0 0 0 0.5 0.5 On 10/4/2023 10:34 AM, Steve Petersen

Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* 24 September 2023 05:22:56 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz External Email - Use Caution Ideally, you

Re: [Freesurfer] Tkregister2 GUI not responding fully

Email - Use Caution I tried adding the –no-surfs (e.g. tkregisterfv --s PI163_noflair --no-surfs),however receive the below error message: ERROR: must spec a moveable volume Many thanks, Viki *From: *freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Date: *Monday, July

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