Re: [Freesurfer] mri_glmfit error

Do you see where it says "ERROR: READ THIS"? And below that do you see that it asks for four things? Can you send those four things? On 10/5/2022 2:51 PM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the fo

Re: [Freesurfer] Quality control of longitudinal recon-all output for >500 participants

If you run mri_segstats --qa-stats subject subject.qa.dat It will generate the QA .dat file. This will have 20 numbers in it. Run mri_segstats --help to see what they are. I usually use #20 (CNR) Run it for all your subjects, then sort by CNR, then examine the worse subjects On 10/4/2022 10:24

Re: [Freesurfer] Getting recon-all stats from SynthSeg 2.0 segmentations

we don't have a way to do this yet. If you want recon-all type stats, you can run synthseg storing the output in subject/mri, then look at the recon-all.log file to get the mri_segstats command that creates the aseg.stats file, modify the command line to use the synthseg output and change the .

Re: [Freesurfer] mri_glmfit error

thickness) 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx Em sex., 30 de set. de 2022 às 13:35, Douglas N. Greve escreveu: almost there -- you did no

Re: [Freesurfer] mri_glmfit error

d --C Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir lh.groupteste.volume.glmdir --eres-save Print of the screen is attached to (3 images). Thank you so much!!! Fernanda Em sex., 30 de set. de 2022 às 11:2

Re: [Freesurfer] mri_glmfit error

That terminal output asks you to send 4 things, but you only sent 2 On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fs

Re: [Freesurfer] tissue type not set in mri_compute_volume_fractions

Your first command should do the trick. What version of FS are you using? The version of that program is over 7 years old. I just ran it with that command line in 7.3.2, and it worked. On 9/28/2022 8:35 AM, Bauer, Martin wrote: External Email - Use Caution Dear Freesurfer experts, I

Re: [Freesurfer] White matter normalization of FLAIR images

If you just want to normalize the flair, you can run samseg on it, ie, samseg --i flair.mgz --o samseg.flair in the output folder you will find a bias corrected volume On 9/28/2022 7:42 AM, James Brown wrote: External Email - Use Caution Dear Dr Bruce, Thank you very much for answerin

Re: [Freesurfer] issue with mris_ca_label and mrisReadTriangleFile

my guess is that your subject is out-of-sync, ie, maybe you edited it and reran part of it (eg, autorecon2) but not all of it (eg, autorecon3) Try looking at the time stamps and or running vno_match_check On 9/27/2022 3:10 AM, Caspar Schwiedrzik wrote: External Email - Use Caution Hi

Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than cross-sectional

Can you send your command line and log file? In particular, how did you register the time points? On 9/26/2022 6:46 AM, Nederpelt, D.R. van (David) wrote: External Email - Use Caution Dear SAMSEG developers, We have a dataset with 55 subjects (MS patients and controls) scanned on th

Re: [Freesurfer] PETSurfer tutorial images?

that's from a tutorial that I never finished. You can get the data from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/sb01.tar.gz https://gate.nmr.mgh.harvard.edu/safelinks/greve/uw.fsf01anat.tar.gz username guest pwd collab On 9/26/2022 12:13 PM, daedalu...@aol.com wrote: Exte

Re: [Freesurfer] Help with group analysis

et. de 2022 às 00:06, Douglas N. Greve escreveu: look at the fsgd examples to see if any fit your situation. Note that the input needs to be something like Input    310211    LR 1    15,5    2,678785 645292,6651    152275,2 ie, "LR" instead of "1", etc using co

Re: [Freesurfer] Help with group analysis

22 1:10 PM, fernanda rohrsetzer wrote: External Email - Use Caution I'm sorry! attached the FSGD file. Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve escreveu: no fsgd file was attached. Also, have you looked at *MailScanner has detected a possible fraud attempt f

Re: [Freesurfer] confirmation of processes/commands used in full processing pipeline

On 9/20/2022 5:01 PM, Harriott, Emily M wrote: External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all doing well. I'm a second-year doctoral student (and beginner FreeSurfer user) trying to use FreeSurfer to segment gray and white matter in 90 T1 imag

Re: [Freesurfer] Help with group analysis

no fsgd file was attached. Also, have you looked at https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi Freesufer's, I need to run a group analysis but I don't know how to do it, the error always a

Re: [Freesurfer] White matter normalization of FLAIR images

it looks like you are using v6. In v6, the flair might not have been normalized On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote: I think you need to add something like -FLAIRpial or -T2pial so it uses it (in which case it will first normalize it), but hopefully someone else can confirm chee

Re: [Freesurfer] SAMSEG - modification of the template files

On 9/25/2022 5:06 AM, Mikolaj Pawlak wrote: External Email - Use Caution On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve wrote: On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote: External Email - Use Caution Would providing better manual segmentations of

Re: [Freesurfer] Sclimbic segmentation error

This is a bug. I've attached a new version. You can copy it to $FREESURFER/python/scripts/mri_sclimbic_seg doug On 9/23/2022 5:29 PM, bar gen wrote: External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. mri_sclimbic_seg --i /Users/mdbarge

Re: [Freesurfer] SAMSEG - modification of the template files

thanks, Mikolaj On Wed, Sep 21, 2022 at 4:01 PM Douglas N. Greve wrote: by template I'm assuming you mean the atlas. There is not an easy way to create a new atlas or modify the existing one (though we are developing methods to do both). For the eyes, you could probably just

Re: [Freesurfer] Running v7 with recon-all v6 files

yes, it is ok On 9/22/2022 8:36 AM, Alexandra Brouillard wrote: External Email - Use Caution Hi I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ‘*permission denied*’ error when typi

Re: [Freesurfer] dcmunpack

Sam way as with unpacksdcmdir, ie, by specifying  -run run subdir format stemname Another way it to use the -auto-runseq format , eg -auto-runseq mgz this will output all the runs preprending the run number and protocol name If you are using 7.3.X, then you can also add --dcm2niix which will spe

Re: [Freesurfer] Fwd: Error

not sure what is going on. It received a kill signal (the 9 mentioned at the end). This often means that it was killed externally. Does this happen repeatedly? Does this happen on other subjects? How much memory did you allocate to your virtual box? On 9/23/2022 1:04 AM, Ahmad Khan wrote:   

Re: [Freesurfer] SAMSEG - modification of the template files

by template I'm assuming you mean the atlas. There is not an easy way to create a new atlas or modify the existing one (though we are developing methods to do both). For the eyes, you could probably just write something to look at the column index in the eyes. If it is less than 128, then set i

Re: [Freesurfer] Longitudinal PET analysis

You may be able to use one of the paired diff options in mris_preproc. Run it with --help. I also put some info on it below. QDEC has been deprecated --paired-diff After concatenating all the inputs together, create a new output file by computing paired differences, ie, Input1-Input2, Input3

Re: [Freesurfer] forcing use of ants-n3 with FS 7.2

Yes, I think so, but look through the recon-all.log file to confirm that it is using N3 and not N4 as I vaguely remember some issue that it would not run N3, but maybe I'm misremembering. On 9/16/2022 11:50 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Just want to c

Re: [Freesurfer] Specifying contrasts for an unbalanced design

Yes, that all looks correct. Good job on a complicated design! On 9/19/2022 12:32 PM, Trolle, Carl wrote: Dear FreeSurfer team, We are investigating if there is a difference in cortical thicknesses between persons with a condition and controls, regressing out the effect of site, sex, age, bu

Re: [Freesurfer] How to modify affine transform if we flip the image in y direction?

the easiest way to think about it is in terms of matrices. You have an affine matrix M already that converts from col,row,slice to xyz. When you flip the 2nd dim, it is like you are applying a matrix R to the new col,row,slice to get the old col,row,slice, so your new affine matrix will be M*R.

Re: [Freesurfer] White matter normalization

can you send your recon-all.log file? On 9/15/2022 4:04 PM, James Brown wrote: External Email - Use Caution Hi Dr Greeve, I ran recon-all using the flag -flair. I couldn't find any command in recon-all.log that normalizes the flair images. It seems just normalization to the T1. I wou

Re: [Freesurfer] Extract Fetal Brain MRI

I don't think that we do. I'm cc'ing Lilla in case she knows On 9/12/2022 6:37 PM, Xuchu Liu wrote: External Email - Use Caution Hi Dear, We are a research team at Rush University Medical Center. We are working on the Fetal MRI data. In this step,*we need to extract the "Fetal Brain

Re: [Freesurfer] White matter normalization

I'm not sure of the order. You can run recon-all passing in the flair with -flair flair.mgz. At some point in the process it will apply a normalization to the flair (it will not necessarily be the same normalization that is applied to the t1) On 9/12/2022 4:01 PM, James Brown wrote:

Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

d: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > Von: freesurfer-boun...@nmr.mgh.harvard.edu > im

Re: [Freesurfer] resample anatomical mask

try mri_convert --downsample 3 input.mgz downsampled.mgz On 9/12/2022 12:54 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to downsample the GM mask, which is at 1mm isotropic voxel size (freesurfer subject space), at 3mm isotropic. What is the m

Re: [Freesurfer] MNI coordinates of minimal thickness in ROI

Once you have the vertex number, you can get the MNI coordinate through some combination of operations shown on this page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems Getting the minimum vertex is a little trickier. I would probably load the thickness into matlab, eg, thickness =

Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

What you show for the lateral ventricle is not really concerning to me. Oftentimes there are differences on border voxels, and border voxels can easily make 5% or more of a structure. If you compare them visually, do you see big differences? On 9/12/2022 7:41 AM, Bernardoni, Fabio wrote:    

Re: [Freesurfer] Issues with recon-all

well, you're running 5.3, which we have not supported in years. My guess is that it has to do with the MNI tools not working in ubuntu. I don't know that you are going to be able to use 5.3 in this context On 9/12/2022 3:01 AM, Hitesh Pradhan wrote: External Email - Use Caution Hello

Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale

HCs always have 0 medicationload so it is not possible to measure a load slope for them. Is it the case that a BD with load=0 is the same as HC? If so, then just have one class. If not, do you expect the age, edu, and tiv slopes to differ between the groups? If not, then use DOSS (default was D

Re: [Freesurfer] recon-all error: ERROR: recon-all command failed with return_code: 1

It is not clear what is going wrong as there is not really an error message.Was there anything printed to the terminal that is not in the log file? The last thing it did was to write out mri/aparc.DKTatlas+aseg.mgz. Can you check that and see if it looks ok? Did you run out of space on the disk

Re: [Freesurfer] SNR

If you have run recon-all on a case, you can use wm-anat-snr to compute the SNR in WM (basically the meanWM/stdWM -- this is not what you are suggesting because it does not use background). You can use freeview to draw your ROIs. You can use mri_segstats to get the mean and std in each ROI On

Re: [Freesurfer] ERROR! FOV=288.000 > 256

Yes, some of the commands inside recon-all do not support a field of view over 256mm, which yours apparently is. I keep meaning to fix this, but we only see it once a year or so and I forget. In any event, just add -cw256 to the command line. On 9/6/2022 10:51 PM, Ellie Shaw wrote: E

Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

My guess is that the variable (G_cingul vol) should be normalized (remove the mean and divide by the stddev). On 9/6/2022 5:44 PM, Piot, Alex wrote: External Email - Use Caution Hello Freesurfer experts, I am trying to perform a GLM, using the volume of a brain region as a covariate

Re: [Freesurfer] Recon-all issue with decompressing in mri_convert step

There might be some issues with jpeg compressed dicom files in 7.2 and before. Can you try using 7.3 to do the conversion with mri_convert or dcmunpack (add -dcm2niix to either one to get the new, better code). On 9/5/2022 10:53 PM, Beatrice Everall wrote: External Email - Use Caution

Re: [Freesurfer] Group Analysis - glmfit results

Campus | Musqueam Traditional Territory *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* August 28, 2022 12:45:22 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer

Re: [Freesurfer] Question about reconall pipeline

first of all, send us the log file On 9/5/2022 8:53 PM, zhoudong...@mail.dlut.edu.cn wrote: External Email - Use Caution Dear FreeSurfer experts: I updated Freesurfer 7.0.0 on my ubantu system, but there is something wrong so that I can't finish running recon-all pipieline.

Re: [Freesurfer] problem with autorecon2-cp

Use both -autorecon1 and autorecon2-cp On 9/2/2022 8:27 AM, Mostafa Fakhri wrote: External Email - Use Caution Hi there, I need just wm.seg.hgz image therefore I used autorecon2-cp: recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject 102109_3T -i /share/users/mfak

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

please include previous emails, otherwise I won't know what "I believe so" refers to On 9/1/2022 3:45 PM, Trolle, Carl wrote: Hi, I believe so, I ran the following commands: mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

You can also  try segment_subregions. This is a python implementation that gives almost exactly the same result (but limited to T2). See https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation It should run on Mac On 8/31/2022 11:28 PM, fsbuild wrote: External Email - Use Caut

Re: [Freesurfer] FSFAST first level covariates

code self as 2 and non-self as 1 so that condition 2 (self*valence) would be different from condition 5 (valence ratings only)? Incredibly helpful, Doug- thank you so much! *From: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Tuesday, August 30, 20

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

f the brain. Thanks, Miriam *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Sunday, August 28, 2022 4:13 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] scl

Re: [Freesurfer] midsagittal mask

mri_cc. Look in the recon-all.log file for an example command line. You may want to change the output file so that you do not overwrite what is there. On 8/31/2022 9:56 AM, Sam W wrote: External Email - Use Caution Hi Bruce, Thank you for the response! Which freesurfer command do I

Re: [Freesurfer] Thalamus segmentation - segmented thalamus looks bigger than brain.mgz would indicate

I don't think the brain.mgz is the right one to look at as it has already been partially segmented. Compare against the norm.mgz (or nu.mgz) instead. It is really hard to determine where the lateral boundaries are in thalamus On 8/31/2022 2:46 AM, Thalhammer, Melissa wrote: External

Re: [Freesurfer] Stepwise recon-all to get volumes

There is not enough information to understand what you did in #2 On 8/30/2022 3:56 PM, Ruifeng Dong wrote: External Email - Use Caution Hi all, I am computing volumetry using freesurfer using two different runs. 1. I just use recon-all -all, and then look at the aseg.stats file. 2.

Re: [Freesurfer] mri_fwhm and diffusion data

I think it should work for b0 images, but I would avoid using any frames that have a gradient. Note that you will need about 10 images to compute the fwhm using mri_fwhm (also make sure you use a mask) On 8/30/2022 1:33 PM, Igor Nestrašil wrote: External Email - Use Caution Dear Free

Re: [Freesurfer] samseg dice score is low

Hi Dilek, your bug report is incomplete. Please see https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to file an informative bug report. On 8/30/2022 12:51 PM, Dilek Özkan wrote: External Email - Use Caution Hello dear all, I use Freesurfer-Samseg for MS lesion segmenta

Re: [Freesurfer] FSFAST first level covariates

associated with the contrast for -a 3 and the contrast for -a 4 would be the same for trials that subjects rate as 1 (self-relevant) vs 0 (not self-relevant)? Could we code it as 2 (self-relevant) and 1 (not self-relevant)? Many thanks!! *From: * on behalf of "Douglas N. Greve"

Re: [Freesurfer] Vertex-wise analysis using ComBat

I don't think you can. I have not looked at combat in a long time, but I thought they did their own GLM. combat might take a design matrix, in which case you could use mri_glmfit and your FSGD to create the design matrix. On 8/30/2022 9:37 AM, Rene Seiger wrote: External Email - Use

Re: [Freesurfer] samseg ground truth's space

If you resample the t1 to another space, it might get blurrier. On 8/30/2022 9:46 AM, Dilek Özkan wrote: External Email - Use Caution I decided to register T1 and Flair to DIR at the beginning. with this way, I will get the new mask in already DIR's space which means manually segment

Re: [Freesurfer] samseg ground truth's space

If you want to  use FSL, you will have to convert to nifit, eg, mri_convert file.mgz file.nii.gz On 8/30/2022 7:01 AM, Dilek Özkan wrote: External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I got the T1 and Flai

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

back and nose) also seems to be the case with participants that sclimbic did work on.. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, August 9, 2022 10:34 PM *To:* frees

Re: [Freesurfer] FSFAST first level covariates

I’m not clear how to get the main effect of valence (brain regions that scale with increasing emotion valence, while holding self-relevance constant)? *From: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Sunday, August 14, 2022 at 1:37 PM *To: *

Re: [Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG

We did fix this at some point. Can you try running the 7.3 version to see if you get the same results? Often multiple threads will yield different results unless specifically programmed otherwise. On 8/27/2022 4:41 AM, Giulio Siracusano wrote: External Email - Use Caution Hi Donatas,

Re: [Freesurfer] Problem with longitudinal processing (MS lesions/samseg)

multivariate lonitudinal atrophy models on the data and need to separate i.e. frontal from parietal cortex. Best Regards Matthias *Von:*freesurfer-boun...@nmr.mgh.harvard.edu *Im Auftrag von *Douglas N. Greve *Gesendet:* Freitag, 24. Juni 2022 16:22 *An:* freesurfer@nmr.mgh.harvard.edu; Cerri

Re: [Freesurfer] T1 gadolinium

Not sure what you are asking or saying. Is Synthseg not useful for gad images or is it useful? On 8/25/2022 10:54 AM, Gonzalo Rojas Costa wrote: > External Email - Use Caution > > Hi: > >SynthSeg is useful for T1-GD volumetric images? Another algorithm, > software? > >Sincerely,

Re: [Freesurfer] Group Analysis - glmfit results

Since this is longitudinal, I'm assuming that your contrast is actually something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might both be less than 0, but if INT is less negative than CON, then C will be positiv

Re: [Freesurfer] Inflating norm.mgz

I'm not sure what you mean by "inflate" here. Do you just mean to run recon-all? Usually, you would run recon-all, then run segmentHA, then register the fMRI to the anatomical (bbregister), then map the segs to the fMRI space (mri_label2vol), then run something like mri_segstats --seg segs-in-f

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

which version of FS are you using? There was a bug in pre 7.3.2 versions. On 8/20/2022 11:05 AM, Fischl, Bruce wrote: Hi Carl Can you upload your subject including the central sulcus labels you drew? Cheers Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Trolle, Carl

Re: [Freesurfer] primary diffusion direction & surface normal vector

you can also Convert a surface file to ascii (vertices are surface normals):   mris_convert -n lh.white lh.white.normals.asc On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal ---

Re: [Freesurfer] Gyrification Index

The "Mean" column will be the mean lGI in the region On 8/17/2022 4:42 AM, Steger Celine wrote: External Email - Use Caution Dear FreeSurfer experts, I try to explore the Gyrification Index of both hemispheres in a population. For this I computed the LGI using the Freesurfer pipeline

Re: [Freesurfer] mri_fill error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 ***

Are you trying to run this from outside of recon-all? If not, can you send the recon-all log file? Also, have you looked at the talairach registration? On 8/15/2022 7:50 AM, 丁晴 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate filled.mgz us

Re: [Freesurfer] FSFAST first level covariates

) And then create a contrast of 2 vs 4 to test the interaction? Would testing contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 vs 0 the main effect of valence? Thanks so much for your help! Angela *From: * on behalf of "Douglas N. Greve" *Reply-To:

Re: [Freesurfer] running mri_glmfit with atlas

Yes, look at the ROI analysis tutorial (eg, asegstats2table or aparcstats2table then mri_glmfit with the --table option) On 8/13/2022 2:22 AM, Hye Min Shin wrote: External Email - Use Caution Hello experts, While going through GroupAnalysis tutorial for freesurfer (*MailScanner has

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

ht at back and nose) also seems to be the case with participants that sclimbic did work on.. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, August 9, 2022 10:34 PM *To:* frees

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

? *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, August 9, 2022 10:34 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left

Re: [Freesurfer] PET-segmentattion

Can you send the terminal output and the petsuv.segstats.dat? How have you verified that the registration is correct? What version of FS are you running? On 8/5/2022 4:44 PM, Bouchra Guelib wrote: External Email - Use Caution I want to segment registered PET to T1 MRI to 45 subcortic

Re: [Freesurfer] Sclimbic segmentation fault error?

not sure. Try running mri_sclimbic_seg --i GP0050/mri/orig.mgz --o junk.mgz On 8/4/2022 4:20 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. It's not being very descriptive abo

Re: [Freesurfer] adding volume to aparc aseg

Try mergeseg. Run with --help to get more info On 8/3/2022 3:41 PM, Benjamin Deck wrote: External Email - Use Caution Hi there, I have extracted an ROI mask for the subthalamic nucleus from MNI space and registered this with the subject's native space orig.mgz I would like to appe

Re: [Freesurfer] Using averaged T1-images to calculate cortical thickness

If I understand correctly, you have one site that acquires two scans, one sag and one axial, and you want to register them together and compute the average, then feed the average to recon-all? Do they have the same isotropic resolution? I'd guess that this would create a systematic artifact.

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

looked ok after that. On 7/28/2022 8:58 PM, Miriam Taza wrote: Nothing strange about them. They’re T1w scans 1x1x1mm3 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, July 28

Re: [Freesurfer] MP2RAGE sequence recon-all

If you are going to pass it the UNI, then you will probably need to mask out the stuff outside of the head. One way to do this is to run samseg on the INV1 or INV2 (INV1 probably better), the run mri_mask uni.mgz seg.mgz uni.masked.mgz Then pass uni.masked.mgz to recon-all On 8/2/2022 8:39 AM, R

[Freesurfer] FreeSurfer 7.3.2 officially released

Hi, at long last we have an official release of 7.3. See the release notes can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and also copied below. Thanks to all who tested the beta version. best doug * Bug fix when converting diffusion tensor data with a negative d

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Can you send us a sample case? On 7/28/2022 8:58 PM, Miriam Taza wrote: Nothing strange about them. They’re T1w scans 1x1x1mm3 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

those look like hcp commands so you should contact them On 7/28/2022 2:00 PM, Ariana Fei wrote: External Email - Use Caution I'm attaching a list of command I used to convert freesurfer cortical thickness output to native space: $Caret5_Command -file-convert -fsc2c "$FreeSurferFold

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

here a log? *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, July 28, 2022 1:27 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] etiv value differs if u

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

iffers a bit from the median, sclimbic module calculates etiv to an extreme. Is this expected to happen? I am concerned if my volumes are incorrect. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Have you looked at the input volume to see if there is anything strange about them? What kind of scans are you passing to it? What is the resolution? On 7/25/2022 9:03 PM, Miriam Taza wrote: External Email - Use Caution Hello, I noticed 20 out of ~240 subjects left basal forebrain vo

Re: [Freesurfer] FSFAST first level covariates

Yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 7/25/2022 6:56 PM, Angela Fang wrote: External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives ar

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

how are you converting them? On 7/27/2022 11:20 AM, Ariana Fei wrote: External Email - Use Caution Hi, We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values

Re: [Freesurfer] Fwd: eTIV

I usually just divide the volume by the eTIV (you can do this in asegstats2table with the --etiv flag). Some people will use it as a nuisance regressor in the GLM On 7/27/2022 3:11 PM, Bouchra Guelib wrote: External Email - Use Caution -- Forwarded message - De : *Bo

Re: [Freesurfer] Understanding ?h.sphere.reg

.reg%2522%26o%3Dnewest> Douglas N. Greve <https://secure-web.cisco.com/1ihiy9xLc9u1yyF8DQ1uOVgvZt_RRMNCUkxXo527aY3PFbUXS3sfC31bcx11dGxVlTccZYSThLDEdA1-3FGQ1CRTg7XrTBcJhZLLtaE0sj3xsYQuQhsTIcoXEHc80x65wcAwmwzAQhBjtjU7gSRcvRovhlCWIQpbERg4NaELK39aLmAdyzCW6rcv0uS1vZXVVEKZpjbIClaZc0KvKcon0XBFT2EnE8V8Wnm

Re: [Freesurfer] Recon-all Error

I'm not sure what is going wrong with that. Can you look at the data? Particilarly the norm.mgz On 7/26/2022 9:53 AM, gianrocco wrote: External Email - Use Caution Hi, I attache hereby my email, as  it was rejected — since I was not registered yet to the list Thanks again Kind

Re: [Freesurfer] ERROR: Talairach failed

website, I found that changing the space is a step of the recon-all, so I used recon-all directly on my original data without any space changing. Thank you so much for your answer. Le lun. 25 juil. 2022 à 03:40, Douglas N. Greve a écrit : did you see where it said "see *MailScanner

Re: [Freesurfer] Group Analysis - FSGD and Contrast

yes, that is the correct interpretation On 7/16/2022 1:00 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Dear experts, I am conducting a group analysis and wanted to confirm that the set up below accurately addresses our research question. Thanks for your help, much

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

e, then it complains interreg: Undefined variable. When I added interreg = 5, then it complains subj: Undefined variable. Should I continue fixing it until no more Undefined variable? *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, July 25, 2022 5

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

arvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, July 25, 2022 5:02 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

my volumes are incorrect. I don't know what you mean. The eTIV in mri_sclimbic_seg should agree nearly perfectly to that in aseg.stats *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

: Undefined variable. Thanks, King-Wai *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, July 25, 2022 1:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Can you copy the attached trac-preproc

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)? On 7/22/2022 8:36 AM, kingwai@gmail.com wrote: External Email - Use Caution Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentTha

Re: [Freesurfer] ERROR: Talairach failed

did you see where it said "see http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

I cannot replicate this on my data. The differences are rather extreme (factors of 3). Can you get us access to the one with the largest difference? YOu can also try regenerating the aseg.stats file, eg, cd subject/ mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/redo.aseg.stats --pv mr

Re: [Freesurfer] Understanding ?h.sphere.reg

The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply a spherical registration, a point on one spherical mesh is mapped to the closest point on the other spherical mesh. not sure if that answers your question ... On 7/21/2022 5:26 PM, Salar Dini, Elaheh wrote: Ext

Re: [Freesurfer] Screenshots in Freeview within a container

If you have the x virtual frame buffer installed, you can run freeview via fsxvfb and it will write your screen shots to a file without bringing up an image (thus the virtual frame buffer). This is available in 7.3 On 7/20/2022 12:40 PM, Garikoitz Lerma-Usabiaga wrote: External Email

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