Re: [Freesurfer] mri_label2label issues

I'm not sure what you did or how to interpret that pic. If I understand, you ran a case through recon-all and created labels on that case. You then recon-all again using a totally different output where you improved the homogeneity. You now want to map the labels you created on the 1st run to t

Re: [Freesurfer] ERROR: niiRead(): error opening file

Do you have proper permissions for it? On 10/22/2021 8:48 AM, g.ton...@libero.it wrote: External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am trying to segment .nii images with FS, using an ubuntu shell in Windows 10. When I run the command "recon-

Re: [Freesurfer] Hard Failures with recon-all

On 10/21/2021 6:59 AM, Wacker, Ewa Helene wrote: External Email - Use Caution Hello FreeSurfer Developers, for my project I am using Freesurfer 7.1 to examine the hippocampal volumes of patients with major depressive disorder (and controls) using the automatic segmentation. Theref

Re: [Freesurfer] Inflated surfaces on FS7 looking different

What platform are you using? On 10/20/2021 11:02 AM, DIANA ORTEGA CRUZ wrote: External Email - Use Caution Dear FreeSurfer team, I am experiencing a display problem in the FreeView version of FreeSurfer 7 for inflated surfaces. The inflated surfaces from my fsaverage folder look as

Re: [Freesurfer] Local GI MRI_segstats error

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, October 18, 2021 9:52 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Local GI MRI_segstats error please send your command line and terminal outout On 10/11

Re: [Freesurfer] ALL atlas and FS-FAST

Not easily. You would have to find a way to map the AAL into the individual subject's space. Then you can just specify that volume and the desired index when running fcseed-config On 10/19/2021 3:24 AM, std...@virgilio.it wrote: External Email - Use Caution Hi is possible to use the

Re: [Freesurfer] Issue with study

have you double checked the orientation of the data in freeview? Eg, is the axial view in freeview truly showing you the axial view of the brain? On 10/18/2021 11:39 AM, Sarkis, Rani A.,M.D.,M.SC. wrote: Hello all, I have an issue with a study, and am wondering whether it can be fixed. Freesurf

Re: [Freesurfer] Topological error on recon after manual edits

You might have introduced a new defect, or just made an existing one worse. If there are topo defects, you can't just ignore them. You don't necessarily have to remove all the dura. Typically there is a "peninsula" where the main WM attaches to the the "island" of dura. All you have to do is cu

Re: [Freesurfer] mri_surf2vol with inflated surfaces

I'm not sure what a ribbon for the inflated surface would look like. You can try mri_surfacemask to create a binary volume of everything inside the surface. On 10/14/2021 7:47 PM, Nicolas Munera Garzon wrote: External Email - Use Caution Greetings freesurfuer community, I've been wo

Re: [Freesurfer] ACPC alignment before processing

Not really. If you pass it an input that is already ACPC, you can add -conform-dc to keep the orientation. On 10/14/2021 9:44 AM, Zhengchen Cai wrote: External Email - Use Caution Hello FreeSurfer Developers, I wonder if we have a function that could automatically align T1w to ACPC

Re: [Freesurfer] Different pixel spacing for scans in the same cohort

it will inevitably create systematic differences On 10/14/2021 8:40 AM, Castro Leal, Gonzalo wrote: External Email - Use Caution External Email - Use Caution Dear Freesurfer, I was wonderign wether processing scans and comparing their stats, e.g. cortical thickness and area,

Re: [Freesurfer] How to obtain parahippocampus segmentations?

Can you send your command line, terminal output, and a list of the files that it did create? On 10/13/2021 4:33 PM, Jingyi Wang wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to obtain parahippocampus segmentations from the "?h.aparc.a2009s.annot" file. How

Re: [Freesurfer] Local GI MRI_segstats error

please send your command line and terminal outout On 10/11/2021 1:36 PM, COLLEEN PLETCHER wrote: External Email - Use Caution Hello, I am trying to run mri_segstats for local GI indices. I am getting a file not found error for /tmp/mri_segstats.tmp.sub-1007_ses_01/.lh.176.ctab I d

Re: [Freesurfer] Creating a surface parcellation from a volume atlas

You can also run recon-all on the mni152, then run. Load it with your volume-based atlas to make sure that the alignment is good and that the surfaces surround your labels, then run mri_vol2surf (--projfrac 0.5) on your volume-based atlas to create a surface-based atlas, then run mris_seg2annot

Re: [Freesurfer] Question about 'thickness.fwhm10.fsaverage'

I don't know what you are asking. Can you elaborate? It is helpful to indclude commanb lines to show how files were created On 10/9/2021 1:30 AM, Dongyue Zhou wrote: External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subj

Re: [Freesurfer] Problem with intensity normalization control points

mask is not being changed from the control points, which volumes do you suggest we use to see white matter changes after multiple edits? Thanks *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve

Re: [Freesurfer] individual analysis and visualization

I don't  know what you mean. Can you elaborate? On 10/8/2021 5:27 PM, Zeng, Qi wrote: External Email - Use Caution Hi Experts, If I want to analyze and visualize baseline and follow-up for an individual subject's change (before-after & after-before).  Should I treat it as a cross-se

Re: [Freesurfer] Question about fsaverage

On 10/8/2021 8:51 PM, Dongyue Zhou wrote: External Email - Use Caution Dear FreeSurfer experts: I want to know cortical thickness in this file 'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in native space. standard Is not the common coordinate sy

Re: [Freesurfer] R: Freesurfer version

8 ott 2021 19:52, Annalisa Lella ha scritto: External Email - Use Caution Pre-processed with recon all Il 8 ott 2021 19:50, "Douglas N. Greve" ha scritto: What do you mean by "elaborated"? On 10/8/2021 1:29

Re: [Freesurfer] glmfit sig file all zeros

he fsaverage in freeview, and verify that it is in the correct location. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Friday, October 8, 2021 10:49 AM *To:* freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] R: Freesurfer version

If you have not done manual editing, then just rerun in 7.2 from scratch On 10/8/2021 1:52 PM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Pre-processed with recon all Il 8 ott 2021 19:50, "Douglas N. Greve" ha scritto: W

Re: [Freesurfer] R: Freesurfer version

o actually it doesn't seem that the results of recon all with version 7 are bugged. Il 8 ott 2021 18:53, "Douglas N. Greve" ha scritto: Sorry, I'm not sure what you are asking when you ask what you should do. Do about what? On 10/4/2021

Re: [Freesurfer] glmfit sig file all zeros

i_glmfit done *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Friday, October 8, 2021 9:25 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] glmfit sig file all zeros what happens

Re: [Freesurfer] Confusion about mean CT measures after registration

You want to measure cortical thickness in standard space? It is not something we typically do, but I guess you could apply the taliarach registration to the surfaces and recompute the thickenss, eg, mris_apply_reg --lta lh.white ../mri/transforms/talairach.lta lh.white.tal mris_apply_reg --lta l

Re: [Freesurfer] Thalamus-proper gone?

It has been replaced by thalamus now On 10/8/2021 6:56 AM, Cubillo, Ana wrote: External Email - Use Caution Dear Freesurfer community, I am using the freesurfer version through a singularity container (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" c

Re: [Freesurfer] Not seeing effects of manual edits and re-running recon-all

same unrelated differences occurred for the wm edits and the wm.mgz still includes the wm edits from before I ran recon-all to correct it. On Oct 1, 2021, at 11:02 AM, Douglas N. Greve wrote: The first thing to do is to re-run you data using different subject names so that you have an

Re: [Freesurfer] error using mri_convert

It might be that the format is too new for our code. Have you tried dcm2niix? We are currently incorporating dcm2niix backend into mri_convert, but we're not there yet. On 10/6/2021 2:36 PM, Rizzo, Nolan W wrote: External Email - Use Caution Hello FreeSurfer developers, I am attempt

Re: [Freesurfer] Fmriprep transform matrix

Sorry, I don't know what h5 format is. On 10/5/2021 4:30 AM, I. Kelleher-Unger wrote: > External Email - Use Caution > > External Email - Use Caution > > Hi there, > > I have used fmriprep to preprocess my BOLD data. One of the outputs of this > pipeline is a T1w-to-MNI transfor

Re: [Freesurfer] Confusion Working with Longitudinal and Group Analysis Tutorials

On 10/4/2021 7:09 PM, Giuseppe Miranda wrote: External Email - Use Caution Hello, I have been looking through tutorials on the website and referencing the freesurfer mail archives, but I am a bit unsure if I am following the correct procedures for my analysis. The main source of co

Re: [Freesurfer] number of seeds in fcseedcor

The frequency of the low pass filter (lpf) must be greater than the high pass filter. Why did you set it to 0? On 9/30/2021 8:27 PM, Nasiriavanaki, Zahra,M.D. wrote: Hi Freesurfer experts, I was wondering how many seeds we can use in fcseedcor command? I have more than 100 seeds and when I us

Re: [Freesurfer] R: Freesurfer version

version 7? Thanks a lot in advance! Annalisa *Da:* freesurfer-boun...@nmr.mgh.harvard.edu per conto di Douglas N. Greve *Inviato:* venerdì 1 ottobre 2021 17:18 *A:* freesurfer@nmr.mgh.harvard.edu *Oggetto:* Re: [

Re: [Freesurfer] A question regarding a Freeview command

The volume is the volume of cortex only, not the volume of subcortical structures. We don't have a VBM-style analysis that would be needed for subcortical GM. You can always do an ROI analysis, asegstats2table and mri_glmfit with --table option; this will allow you to analyze the volume of each

Re: [Freesurfer] Comparing volumes before and after editing

If you subtract them, eg, fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz This command will subtract the two, take the absolute values, then threshold (binarize) the differences. I'm not sure what you are looking for in terms of aparc+aseg, but you can do something like mri_segstats --ctab-

Re: [Freesurfer] matlab: command not found - How can I solve this?

You need to add matlab to your path. If you type which matlab it will indicate whether it is in your path or not On 10/1/2021 3:51 PM, Camila Fernandes da Silva wrote: External Email - Use Caution Hey, I'm totally new into Freesurfer and I need some help with my Matlab. I tried to do "

Re: [Freesurfer] Problem with intensity normalization control points

The wm.mgz is expected since we added denoising to it; but it does not matter because wm.mgz is essentially a binary mask of WM. The brainmask.mgz is created from T1.mgz. The T1.mgz will be affected by control points, but only if you run it from the beginning. The surfaces are placed on brain.f

Re: [Freesurfer] Brodmann areas volumetric parcellation freesurfer 6.0

Look in the recon-all.log file for the command that creates the aparc+aseg.mgz. Change the annotation to be the annotation that you want to use, and change the name of the output file. On 9/30/2021 10:07 AM, Ahmed Radwan wrote: > External Email - Use Caution > > Dear FreeSurfer experts,

Re: [Freesurfer] Repeated measures analysis

Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 9/30/2021 1:08 AM, Abbie Taing wrote: External Email - Use Caution Hi all, I have a between subjects factor (3 groups) and within subjects factor (3 stimuli type). I am interested in comparing cortica

Re: [Freesurfer] glmfit sig file all zeros

    0.5000                -0.   1.  -0.     3.                -0.  -0.  -0.     1. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, September 23, 202

Re: [Freesurfer] SAMSEG output orientation not the same as input images

Can you compare the template_coreg.mgz to the input image; they should be mostly aligned. If not, then the initial registration failed. On 9/28/2021 2:38 PM, daedalu...@aol.com wrote: External Email - Use Caution We have recently installed FS-7.1 and have tested a few “ADNI” images

Re: [Freesurfer] inter-hemispheric registration

Check out 1.3 in https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 9/28/2021 4:07 AM, Yu-Chi Chen wrote: External Email - Use Caution Dear FreeSurfer experts, My current analysis is for analyzing the vertices of the cortical surfaces. I'd like to have the same vertice numbers of th

Re: [Freesurfer] Not seeing effects of manual edits and re-running recon-all

The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing On 9/27/2021 7:16 PM, Kevin Miller wro

Re: [Freesurfer] Control for eTIV on Voxelwise Wholebrain Analysis?

Yes. Alternatively, if you are using mris_preproc, you can add --etiv to the command line and it will do the correction by dividing by the eTIV (rather than using a regressor). On 9/27/2021 2:51 PM, Wakim, Kathryn-Mary wrote: External Email - Use Caution Hi all, I'm currently runni

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

same thing On 10/1/2021 11:42 AM, Aaron Tanenbaum wrote: External Email - Use Caution What about for 7.1? On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: What version are you running? In 7.2, it will automatically set the t2pia

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

What version are you running? In 7.2, it will automatically set the t2pial flag when you specify -t2 On 9/27/2021 11:53 AM, Aaron Tanenbaum wrote: External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag? ___

Re: [Freesurfer] Freesurfer version

The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thick

Re: [Freesurfer] Color LUT after coregister and reslice aparc/aseg.nii

How did you reslice? If you used trilinear interpolation, then that would mess up the values; use nearest neighbor. Also, check out PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer which can do this sort of thing in a principled way On 9/27/2021 11:17 AM, Ryan Wales wrote:

Re: [Freesurfer] Converting MNI to RAS on fsaverage

No, the RAS in fsaverage is in MNI305 space, so no need to do the conversion. On 9/27/2021 11:22 AM, Kennedy, Bryan wrote: Good morning, We are trying to conduct a meta-analysis by mapping reported MNI dimensions (by others) on fsaverage. I know that I have to use the following conversion:

Re: [Freesurfer] glmfit sig file all zeros

It looks like the mask is the wrong size. What is the dimension of /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz you can check with mri_info On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote: Hi, I am running glmfit on some functional data (usi

Re: [Freesurfer] Announcing FreeSurfer version 7.2

inting out. Both of those surfaces should be tessellated at 1mm, but I just see the white and pial. Thanks! Corinna On Wed, Jul 21, 2021 at 1:49 PM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Yes, just run recon-all with the -fill option to regenerated the filled.mgz

Re: [Freesurfer] How to get cortical volume from a particular atlas?

Sorry, we don't support that atlas. Have you tried contacting FSL? On 9/23/2021 7:08 AM, DRON Noramon wrote: External Email - Use Caution Dear Freesurfer Team I have a very naive question. I am in urgent need to get a cortical region volume base on the Harvard-Oxford Cortical Atlas(f

Re: [Freesurfer] Migrating data from v6 to v7

You don't need the -legacy flag. Just make a copy of your v6 data and then run recon-all -all -s subject It will see and apply your previous edits. On 9/22/2021 2:14 AM, Amanda Boyes wrote: External Email - Use Caution Hi FreeSurfer experts, Just checking whether anyone has any advi

Re: [Freesurfer] Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.

They are only changed as part of the resampling process (ie, a form of interpolation). Volume and surface area are jacobian corrected. On 9/22/2021 1:24 AM, 周冬跃 wrote: External Email - Use Caution Dear FreeSurfer experts: I use the command recon-all qcache to get file sub_01/surf/lh

Re: [Freesurfer] QDEC command not found

We are no longer supporting qdec On 9/21/2021 2:15 PM, Fabiola Macruz wrote: External Email - Use Caution External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all th

Re: [Freesurfer] Freesurfer version confusion

Did the size of the defect change? On 9/19/2021 8:36 PM, Paul, Rahul wrote: Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fi

Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

zero value for each input *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Wednesday, September 15, 2021 1:19 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR Can't see the image. Can you just c

Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

Can't see the image. Can you just cut-and-paste the full terminal output into the email? On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote: External Email - Use Caution Dear Freesurfer Team, I have been struggling with an error using the mri_gmfit command. I have been trying to run a s

Re: [Freesurfer] Samseg Choroid Plexus Segmentation T1 and T2-FLAIR separate argument

There is not, but you could create your own. By default, it uses this table to determine which superclass each segment goes into $FREESURFER/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/sharedGMMParameters.txt YOu can see that CP is in the CSF glass. You can try creating its own

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 1

I can't tell what the problem is. Have you looked at your images in these cases to see if there  is anything wrong with them? What resolution is your data? On 9/14/2021 1:59 PM, Xiong, Yanyu wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recond

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 functio

Re: [Freesurfer] Calculating GMV

On 9/13/2021 10:11 PM, Brigitte Pace wrote: External Email - Use Caution We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calcula

Re: [Freesurfer] Different volume measurements Freesurfer V7.1.1

First, make sure you are not running into this problem https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes The global morphometry statistics embedded in aseg.stats and other files have an error when the input volume has a voxel resolution different than 1mm^3. See MorphometryStats

Re: [Freesurfer] Update FS version and manually edited controls

You should just make a copy of your subject, then re-run with version 7x. It should automatically see the edits and incorporate them. On 9/13/2021 3:40 PM, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I have a collection of older controls that I have reconstr

Re: [Freesurfer] Cortical thickness difference as vertex-label overlay

Try mri_mask yourcontrast/gamma.mgh sig.masked.mgh yourcontrast/gamma.masked.mgh gamma is the contrast value (eg, patients minus controls). Is that what you wnat? On 9/10/2021 6:20 AM, Graterol Pérez, José Alberto wrote: External Email - Use Caution Hello, I've done a group compari

Re: [Freesurfer] unpacking Diffusion data

can you point me to the data? On 9/8/2021 12:46 PM, Nasiriavanaki, Zahra,M.D. wrote: Hello Freesurfers, I have  6 runs of DTI data per subject in a sample of 50, and I want to unpack the dicoms, so it outputs the bval bvec values, to use in dt_recon. I realized I can use either dcm2nii or mr

Re: [Freesurfer] recon-all terminated by signal 11 at various points (eg. mri_normalize, mris_place_surface)

Not sure what is going wrong. Have you looked at your images? Eg, try freeview orig.mgz aseg.presurf.mgz It is a bit unusual that it is dying in two different places on the same data. On 9/8/2021 3:39 AM, Falko Mecklenbrauck wrote: External Email - Use Caution Dear Freesurfer Develop

Re: [Freesurfer] preproc-sess output

You'll have to load it as an overlay to a surface, eg, freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay=fmcpr.up.sm5.fsaverage.lh.nii.gz there won't be much to see :) On 9/8/2021 5:51 AM, Alice Giubergia wrote: External Email - Use Caution Dear Freesurfer's e

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

yes, in the process now of upgrading. We'll use dcm2niix internally. On 9/7/2021 5:11 PM, Fischl, Bruce wrote: Our dicom reader is probably too old Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Peled, Noam *Sent:* Tuesday, September 7, 2021 2:56 PM *To:* Freesurfer su

Re: [Freesurfer] XL defect detected_how to resolve

Find the defect and edit it out of the wm.mgz (or the filled.mgz if using 7.2). See the tutorial on fixing defects On 9/6/2021 12:23 AM, Koustav Chatterjee wrote: External Email - Use Caution Dear Forum members, Could you please help me resolve the following issue? The recon-all.log

Re: [Freesurfer] TOPOLOGICAL DEFECTS

that is in ventricle, so you don't need to edit it (unless it is creating such a big topological defect that FS is crashing or taking a really long time) On 9/4/2021 1:05 PM, halil ibrahim AKÇAY wrote: External Email - Use Caution Hi My name is Halil Ibrahim akçay. I am a neurologist

Re: [Freesurfer] Issue with reg-feat2anat and tkregister2

I think I fixed this in 7.2. Can you try that? On 9/3/2021 12:11 PM, ChristianBauer wrote: External Email - Use Caution Hello freesurfer help team! I am using the command reg-feat2anat but I get the error message: tkregister2_cmdl_cmdl: Command not found. Here is my full command

Re: [Freesurfer] FreeSurfer Visualization Questions

On 9/3/2021 9:28 AM, Junyeon Won wrote: External Email - Use Caution Dear Freesurfer experts, Could I have a couple of questions regarding visualization? 1) I found significant clusters on the right hemisphere volume after glm_fit and cluster correction. I would like to extract the

Re: [Freesurfer] Recon-all error: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage

What platform are you using (eg, mac?). Can you send the recon-all.log file? Can you verify that the file actually exists and that you have read permissions? On 9/3/2021 4:52 AM, Szulia Agata wrote: External Email - Use Caution External Email - Use Caution Hi, I have a pro

Re: [Freesurfer] Question about freesurfer

I don't know about using R. In FreeSurfer you can run asegstats2table (for aseg.stats) or aparcstats2table (for aparc.stats). Run with -h to get help or look at our tutorials On 9/2/2021 7:26 AM, hyeyoung park wrote: External Email - Use Caution Hi, This is hyeyoung Park from Seoul N

Re: [Freesurfer] How to remove segments from white and left cerebral white matter and get cerebral white matters without these segments

Not sure whey those are there. Why not just create your WM mask with mri_binarize --i aseg.mgz --match 2 4 --o wm.mask.mgz On 9/1/2021 8:37 PM, Ammar Shujaa wrote: External Email - Use Caution Hello freesurfer developer, I have extracted the right and left cerebral white matter (labe

Re: [Freesurfer] Total Brain volume normalization

No, this was a situation that we were not anticipating. You'll have to do it yourself. If you run asegstats2table, it will create a table that has the BrainSegNotVet and the eTIV On 9/1/2021 4:19 PM, Fabiola Macruz wrote: External Email - Use Caution External Email - Use Cau

Re: [Freesurfer] Mask Correlation Analysis Area by Yeo Network

you can use the --mask or --label options. You can create a single label by breaking up the yeo annot into individual labels (mri_annotation2label), then combining the ones you want (mri_mergelabels) On 8/31/2021 6:13 PM, Haley Park wrote: External Email - Use Caution Hello, I would

Re: [Freesurfer] SAMSEG esitmation error

Not sure. The first step would be to check the affine registration with freeview template_coregistered.mgz input where input is the input to samseg On 8/31/2021 5:27 AM, achille.teil...@chu-lyon.fr wrote: External Email - Use Caution Dear experts, We are working with a large MRI datas

Re: [Freesurfer] TOPO_DEF

Are you asking if that  is a topological defect? It is impossible to say from one slice. The surface itself is ok to be there as that is on the medial well. On 8/30/2021 8:53 PM, halil ibrahim AKÇAY wrote: External Email - Use Caution Hi My name is Halil Ibrahim akçay. I am a neurolo

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 11

can you send the recon-all.log file? On 8/30/2021 3:54 AM, 朱子家 wrote: > External Email - Use Caution > > Hello FreeSurfer Developers, > > when I run the recon-all command: > > $ export SUBJECTS_DIR=`pwd` > $ cd /lustre/home/acct/zjzhu/project/zzu_MRI/T1/test > $ ls *nii | parallel --jobs

Re: [Freesurfer] recon-all exited with ERRORS

Not sure what you are trying to do. Usually we do not do voxel-wise analysis on the asegs (eg, like with a vbm) On 8/29/2021 2:52 PM, guang wrote: External Email - Use Caution At 2021-08-05 08:44:11, "guang" wrote: Hello FreeSurfer Developers, I'm trying to analyze ase

Re: [Freesurfer] WM or Pial edits to correct surfaces

Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface.  I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is du

Re: [Freesurfer] Problem, recon-all never finishes (it gets stuck)

What kind of 7T image is it? Often they have terrible bias fields. Have you looked at the images with the ?h.orig.nofix surfaces? Also, remember to send your recon-all.log files. On 8/27/2021 10:43 AM, Samuel Paré wrote: External Email - Use Caution Hi, I have been trying to process

Re: [Freesurfer] PCA

The simple answer is yes with mri_glmfit --y func.nii.gz --mask yourbrainmask.mgz --osgm --pca --o glm then look in the pca folder However, this will only have the mean removed. If you want fancier detrending, you'll have to work a bit harder. On 8/27/2021 3:59 AM, std...@virgilio.it wrote:  

Re: [Freesurfer] Isolate Function Error

It looks like label 7 was not in the volume. Where did aparc+aseg.nii come from? On 8/26/2021 1:37 PM, A.R. Sekar wrote: External Email - Use Caution External Email - Use Caution Hello Experts, Hope you are well! I am trying to extract ROIs from the aparc+aseg file after ru

Re: [Freesurfer] Error messages when trying to start Qdec

qdec is deprecated. Use the "command line" stream instead (ie, mris_preproc, mris_surf2surf, mri_glmfit, and mri_glmfit-sim) On 8/24/2021 4:44 AM, inbal paran wrote: External Email - Use Caution Dear FreeSurfer experts, I recently started to work with freesurfer and I am now trying t

Re: [Freesurfer] Periaqueductal gray (PAG) volume

No, it does not. On 8/23/2021 11:28 AM, Alan Francis wrote: External Email - Use Caution Hi Doug et al, I know that this question may have been asked before, but does the latest version of FS segment/ parcellate the volume of the periaqueductal gray (PAG? Thank you, Alan -- /|~|

Re: [Freesurfer] Run script

you have to be in the same folder as lh.Yeo2011_17NetworksConfidence_N1000.mgz On 8/22/2021 5:40 PM, Haley Park wrote: External Email - Use Caution Hello, I got a response to a question I asked earlier to run the following script: mri_convert lh.Yeo2011_17NetworksConfidence_N1000

Re: [Freesurfer] BrainSegVol above 2 mio mm³

This is a known issue. See https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Known Issues: The global morphometry statistics embedded in aseg.stats and other files have an error when the input volume has a voxel resolution different than 1mm^3. Check and see if th

Re: [Freesurfer] Base correction, longitudinal analysis

That command will re-run the base, but it should respect your edits. Is that not the case? If you just want to re-run part of it, you can specify the stage (eg, -autorecon2) instead of -all On 8/18/2021 8:05 PM, Eszter Boros wrote: External Email - Use Caution Thank you for your answ

Re: [Freesurfer] 回复: FreeSurfer questions exchange

, and want to perform cortical surface parcellation on them to generate label files and .annot files,    how can I do it? Thank you! *发件人: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> *发送时间: *2021年8月18日5:27 *收件人: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] FSFAST (mkcontrast-sess) with Octave

Hi Lauri, I was able to run this successfully here on 7.2. What version of FS are you using? Can you send /tmp/mkcontrast2.28236.m (if still there)? doug On 8/17/2021 3:10 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Dear Surfers, > I am trying to run fsfast mkcontrast

Re: [Freesurfer] LGI - trouble creating output file for each subject

It says that it cannot find /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white does that file exist and readable? On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caut

Re: [Freesurfer] FreeSurfer qcache Inquiry

By default, the measure list includes the .K and .H files. You can specify your own list of measures with the -measure option. Eg, -measure thickness (you can add more -measure options for more measures) On 8/13/2021 5:10 PM, Junyeon Won wrote: External Email - Use Caution Dear Free

Re: [Freesurfer] INSULA

We don't have post vs ant insula, but have you looked at the aparc.2009s.annot? It has a much finer insula segmentation. You might be able to merge some of those labels to get what you want. Otherwise, you can split the big insula label in the aparc with mris_divide_parcellation On 8/13/2021

Re: [Freesurfer] longitudinal LME stats

On 8/11/2021 1:17 PM, Erik O'Hanlon wrote: External Email - Use Caution External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and

Re: [Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?

Yea, I've tried that before. It does not work very well. You can proceed, but it will not be providing you with a very good correction. On 8/9/2021 9:30 AM, Shane Schofield wrote: External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 w

Re: [Freesurfer] FreeSurfer questions exchange

On 8/9/2021 5:51 AM, 刘 亚飞 wrote: External Email - Use Caution Hello! In the process of learning freeSurefer, I have two questions: The first question is that I want to convert a file in .stl format to a .pial file, but the error "does not apear to be an STL file" appears when usin

Re: [Freesurfer] Fwd: Base correction, longitudinal analysis

That is just part of the way the long stream works. When you run a base subject, you have to spec all the cross tps that go into it. I agree, it is not elegant. On 8/8/2021 8:03 PM, Eszter Boros wrote: External Email - Use Caution Dear FreeSurfer Team, I am working on a longitudinal

Re: [Freesurfer] qcache option for post recon-all longitudinal data

On 8/6/2021 6:35 PM, Zeng, Qi wrote: External Email - Use Caution Hi Freesurfer experts, I've done running a longitudinal analysis pipeline for individuals in 3 groups. Now, I need to get prepared for QDEC group analysis. I cp all groups of individuals to the same directory and eac

Re: [Freesurfer] Creating an Freesurfer .annot file from an MNI coordinate region of interest

First, try running recon-all on the mni152 template Find the vertex closest to your seed coordinate You can create a circle on the surface with something like this (where vertexno is the vertex number you found above) mri_volsynth --dim nvertices 1 1 1 --pdf delta --delta-crsf vertexno 1 1 1 --o

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