Re: [Freesurfer] SynthSR problem

External Email - Use Caution Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use code built with Intel processor specific instructions that cannot run on an arm processor, i.e., there is not full backwards binary compatibility in that case using the Rosetta

[Freesurfer] SynthSR problem

External Email - Use Caution Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o

[Freesurfer] mri_synthseg problem with CT... freesurver v 7.3.2

External Email - Use Caution Hi: I downloaded some CT from OASIS 4 database... I tried to segment it using mri_synthseg (freesurfer v 7.3.2)... But I got bad results... Only I got the segmentation of one region of the brain... Also, I do the crop of the image, and the threshold

[Freesurfer] WG: Problem with recon-all --> nii.gz file not found

External Email - Use Caution Von: Rühr, Livia Gesendet: Donnerstag, 12. Januar 2023 17:25 An: freesurfer@nmr.mgh.harvard.edu Betreff: Problem with recon-all --> nii.gz file not found Dear Sir or Madame, for my thesis I am running recon-

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

-server-release-notes%2F%3Fsource%3DFastX3-3.2.34 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng Date: Saturday, 19 February 2022 at 1:28 am To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

February 2022 8:25 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do y

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use? Ruopeng On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones mailto:h.dempseyjo...@uq.edu.au>> wrote: External Email - Use Caution Hi there, I am having a weird

[Freesurfer] Fw: Problem when using freesurfer

External Email - Use Caution Dear Sir or Madam, Hope you are doing well! Thank you very much for your contribution to the freesurfer software which offers great help to research in the neuroimaging area. However, I met a problem when using it and I hope you can help me with it.

Re: [Freesurfer] A problem about Freesurfer

no, humans only. Though if you google around you might find someone who has adapted it On 6/4/2021 4:33 AM, 胡俊涛 wrote: External Email - Use Caution Can I use Freesurfer to process MRI image data of mice? Thank you! ___ Freesurfer

[Freesurfer] A problem about Freesurfer

External Email - Use Caution Can I use Freesurfer to process MRI image data of mice? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tkregister2 problem on its GUI

Try using tkregisterfv instead (it takes all the same command line args but uses freeview On 5/28/2021 2:13 AM, 张威 wrote: External Email - Use Caution Hello Freesurfer developers, I am attempting to manually register a cerebral blood flow images to a T1 weighted images via the

Re: [Freesurfer] Decompressed problem during reconall

Can you send the log file of the run using the nifti as input? The file you attached is for  dicom input. On 4/8/2021 8:39 AM, Banu Femir wrote: External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7

Re: [Freesurfer] mri_convert problem

, 2021 at 11:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert problem External Email - Use Caution Dear List, I have installed the ubuntu version of freesurfer (creating the VM as in the tutorial) I would like to run the following command: mri_convert -c -oc 0 0 0

[Freesurfer] Decompressed problem during reconall

External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I had the identical problem (failure at segmentation stage, as described below) in 4 subjects of my dataset. I have no possibility to run analyses on a linux machine… Since all 4 subjects had no problem using Freesurfer 6, is it so wrong

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi doug, I tried to re-run 3 or 4 times and always failed at the segmentation stage… I have no linux machine, but I can try in a mac computer with a different OS... thank you! Angela > Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve > ha

Re: [Freesurfer] LGI problem

Hi Angela, I cannot replicate this error. If you re-run, does it always exit with error? You can try this quickly be running setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen cd /Users/angelafavaro/Desktop/Aachen/subj220/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta

Re: [Freesurfer] LGI problem

External Email - Use Caution I have uploaded to you the data using the Martinos Center FileDrop Hope is a good option for you Thank you Angela > Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro > ha scritto: > > External Email - Use Caution > > > Hi

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working... I am trying to

Re: [Freesurfer] LGI problem

Hmmm, I don't know. Can you upload the data set? Follow these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name:

Re: [Freesurfer] LGI problem

Someone just pointed out that I posted the wrong file. Here is the correct one. Copy it to the same folder https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m On 5/13/2020 11:01 PM, Douglas N. Greve wrote: Download this file

Re: [Freesurfer] LGI problem

Download this file https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m and copy it into $FREESURFER_HOME/matlab and rerun. Let me know if that fixes it. On 5/13/2020 5:57 PM, Angela Favaro wrote: External Email - Use Caution Please find attached

Re: [Freesurfer] LGI problem

Are you running this from recon-all? If so send the recon-all.log. If from the command line, send the command-line and all terminal output On 5/13/2020 5:28 PM, Angela Favaro wrote: External Email - Use Caution Hi Doug! yes, it run under version 6! Please let me know if it is

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug! yes, it run under version 6! Please let me know if it is something that can be solved Thank you Angela > Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve > ha scritto: > > Does it run under version 6? We are not really supporting

Re: [Freesurfer] LGI problem

Does it run under version 6? We are not really supporting lGI anymore, but maybe we can get it to work On 5/13/2020 4:24 PM, Angela Favaro wrote: External Email - Use Caution Hi all, I am using the new version of Freesurfer 7.1.0 And I am finding problems in running gyrification

[Freesurfer] LGI problem

External Email - Use Caution Hi all, I am using the new version of Freesurfer 7.1.0 And I am finding problems in running gyrification analysis. I have Matlab 2016a (and 2019b) with the toolbox image processing The error is after the command find_corresponding_center_FSformat

[Freesurfer] Segmentation problem

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm

Re: [Freesurfer] Thickness problem

sig = -log10(p)*sign(contrast), so if p=.01, then sig=2. The sign(contrast) is the direction of the contrast On 12/19/2019 4:14 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your comment. I compared cortical thickness bewteen two groups. I have a

Re: [Freesurfer] Thickness problem

External Email - Use CautionHi Dr. Greve, Thank you for your comment.I compared cortical thickness bewteen two groups. I have a question. What does the values mean in the "sig.table.dat" file (ex. 0.571)? Good luck,   

Re: [Freesurfer] Thickness problem

Can you try running the ROI results with mri_glmfit? ie, if you ran aparcstats2table to get the ROI results you input to SPSS, then run mri_glmfit --table table.dat --fsgd g1v4.fsgd --C group.diff.mtx --glmdir table.g1v4.glmdir where table.dat is the result of aparcstats2table Then look at

[Freesurfer] Thickness problem

External Email - Use CautionHi there, I obtained results for right thickness using aparcstats2table.Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. A group showed higher right thickness in the superior

Re: [Freesurfer] the problem about XL defect detected...

Use orig.nofix and orig instead On 4/12/2019 4:21 AM, Abby tang wrote: External Email - Use Caution Hi， I am sorry. In my recon_all folder, there isn't lh.white, rh.white,lh.pial and rh.pial files, so I can run below command freeview -v topo_defect_before/mri/brainmask.mgz \

Re: [Freesurfer] the problem about XL defect detected...

External Email - Use Caution Hi， I am sorry. In my recon_all folder, there isn't lh.white, rh.white,lh.pial and rh.pial files, so I can run below command freeview -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f

Re: [Freesurfer] the problem about XL defect detected...

check out https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview On 4/11/19 10:58 AM, Abby tang wrote: > > External Email - Use Caution > > Hello FreeSurfer Developers, I'm attempting to recon-all subjects but > for some of my subjects I get the following error

[Freesurfer] the problem about XL defect detected...

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) XL defect detected... Killed Linux

Re: [Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > Dear Douglas, > > I wanted just to compute rescaled PET image without any PVC but > following the same process as if I would have applied PVC. Moreover, I > didn’t want to reduce FOV with auto mask

[Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

External Email - Use Caution Dear Douglas, I wanted just to compute rescaled PET image without any PVC but following the same process as if I would have applied PVC. Moreover, I didn’t want to reduce FOV with auto mask generated (to still be in the gtmseg space). So I ran the

Re: [Freesurfer] segmentation problem

Hi Manuela you can certainly do manual editing in freeview cheers Bruce On Thu, 10 Jan 2019, Manuela Costa wrote: External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation.  Unfortunately,

[Freesurfer] segmentation problem

External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation. Unfortunately, this subject has a large lesion in the right hemisphere. Looking at the aseg, the segmentation of the bilateral amygdala

[Freesurfer] Fwd: problem with contrast in 1st-level analysis

External Email - Use Caution I also tried anther task-related fMRI, which has similar parameter, list as follow: 0 1 16 1 move 17 0 16 1 blank 33 2 16 1 static 49 0 16 1 blank 65 1 16 1 81 0 16 1 97 2 16 1 113 0 16 1 129 1 16 1 145

Re: [Freesurfer] mris_fwhm problem

No, not in the current framework. Even if there were, fwhm=.66 would not give you much smoothing. The intervertex distance is about 1mm, at fwhm=.66mm, the nearest vertex would be about 3 standard deviations away, meaning that the smoothing would be minimal. On 12/21/18 12:12 PM,

Re: [Freesurfer] mris_fwhm problem

So, is there anyway around this issue? > > The smoothing works through iterative nearest neighbor smoothing, so the > fwhm is essentially discretized because you can't have fractions of an > iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 > iteration, so it chooses 0. > > On

Re: [Freesurfer] mris_fwhm problem

The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0. On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu

[Freesurfer] mris_fwhm problem

Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command: mris_fwhm --s --hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask

Re: [Freesurfer] freeview problem on Linux RHEL 7-4 libGLU.so.1

I get this message when trying to run an example: > > > > *"freeview.bin: error while loading shared libraries: libGLU.so.1: cannot > open shared object file: No such file or directory*" > > > I installed the missing library and now it is in >

Re: [Freesurfer] mris_register problem

to increase the angular search range in the affine part to get it to work.   Cheers,   Chris.   From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_register problem   Hi Chris

Re: [Freesurfer] mris_register problem

list Subject: Re: [Freesurfer] mris_register problem Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote

Re: [Freesurfer] mris_register problem

Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote: External Email - Use Caution

[Freesurfer] mris_register problem

External Email - Use Caution Freesurfer experts, I'm having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and

[Freesurfer] The Problem Using "mris_ca_train"

External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run

Re: [Freesurfer] combinesurfs problem: shifts and rotates

t; > -Oorspronkelijk bericht- > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N. Greve > Verzonden: 3 mei 18 0:08 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] combinesurfs problem: shifts

Re: [Freesurfer] combinesurfs problem: shifts and rotates

Does it work if you don't save it as an stl file? On 05/02/2018 06:39 AM, Klink-3, N.E.C. van wrote: > > > Dear all, > > I am struggling with coverting and combining pial surfaces back to > native space. My result is 90 degrees rotated, and shifted from the > original MRI. > > The initial

Re: [Freesurfer] Surface Problem

[Freesurfer] Surface Problem Z K zkaufman at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Surface%20Problem=%3C253ef8e4-8ac6-18e9-86f7-f2945cbeba69%40nmr.mgh.harvard.edu%3E> Wed Jun 21 16:28:19 EDT 2017 * Previous message: [Free

Re: [Freesurfer] Subparcellation Problem

Also, I'm using Freesurfer 5.3 On Wed, Apr 11, 2018 at 1:50 PM, Connor Garris wrote: > Hello, > > I'm running into a problem when subparcellating my regions of interest > where after subparcellating there are some sublcusters that are labelled > identically by freesurfer

[Freesurfer] Subparcellation Problem

Hello, I'm running into a problem when subparcellating my regions of interest where after subparcellating there are some sublcusters that are labelled identically by freesurfer even though they are distinct subclusters. More specifically, I ran one iteration of mris_divide_parcellation passing it

Re: [Freesurfer] Installation problem

| sort thanks, Andrew From: Neda Mohammadi <n55moham...@gmail.com> Date: Sunday, March 11, 2018 at 6:30 AM To: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Cc: FS Help <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Installation problem Hi Andrew, Than

Re: [Freesurfer] Installation problem

Hi Andrew, Thanks for your reply. It repeat the freesurfer startup message . freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast

Re: [Freesurfer] Installation problem

Hi Neda, What’s going on exactly? Is the source command hanging or is it repeatedly printing the freesurfer startup message? best Andrew On March 7, 2018 at 3:03:38 AM, Neda Mohammadi (n55moham...@gmail.com) wrote: Dear Expert, I tried to install Freesurfer

[Freesurfer] Installation problem

Dear Expert, I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps: 1. Download and extract into the directory /usr/local 2.export FREESURFER_HOME=/usr/local/freesurfer Its fine, but when I run this step 3.source $FREESURFER_HOME/SetUpFreeSurfer.sh I receive this message n

Re: [Freesurfer] T1 problem after reprocessing

I loaded the control.dat file and can't find any control points in that corner. On Wed, Dec 20, 2017 at 2:07 PM, Douglas N Greve wrote: > It looks like you may have put a control point up in the corner. Can you > verify that this is not the case? > > > On 12/20/2017

Re: [Freesurfer] T1 problem after reprocessing

It looks like you may have put a control point up in the corner. Can you verify that this is not the case? On 12/20/2017 02:18 PM, Romella Durrani wrote: > Hi, > > I'm having problems with T1 after reprocessing. The original scan has > no problems on T1 (screenshot attached), but after I

Re: [Freesurfer] Freeview problem: ROIs showing in wrong slice when loaded with certain volumes

Hi Sara, Would it be possible to send me the files and the freeview command you ran? Best, Ruopeng > On Dec 6, 2017, at 6:16 PM, Sims, Sara A wrote: > > Hello, > I am having an issues with freeview ROIs. When I use the command line to load > the orig and the ROIs by

[Freesurfer] Freeview problem: ROIs showing in wrong slice when loaded with certain volumes

Hello, I am having an issues with freeview ROIs. When I use the command line to load the orig and the ROIs by themselves they display correctly, however when I display the orig volume and the volume versions of the ROIs- the label ROIs suddenly change to be in the wrong plane. I have done this

[Freesurfer] dmrirc.tutorial problem

Dear experts, I try to run trac-all -bedp -c dmrirc.tutorial, but error shows like this, then stop: INFO: SUBJECTS_DIR is /HD4/DTI INFO: Diffusion root is HD4/DTI Actual FREESURFER_HOME /HD2/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this

[Freesurfer] freeview problem on Linux RHEL 7-4 libGLU.so.1

/usr/local/fsl/bin/FSLeyes/libGLU.so.1 any idea ho to solve this problem Thanks avner ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is int

Re: [Freesurfer] tracula problem

...@nmr.mgh.harvard.edu] on behalf of Lin, Yizhi [l...@union.edu] Sent: Monday, August 07, 2017 3:57 PM To: Freesurfer support list Subject: [Freesurfer] tracula problem I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel

[Freesurfer] tracula problem

I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC

[Freesurfer] Matlab Problem LME

Dear FreeSurfer experts, I am following the LME tutorial for the spatiotemporal mass-univariate model on Matlab 8.2. When I get to the point where the covariance estimates are segmented into homogeneous regions I run into a problem. Nothing really happens in Matlab anymore. This is my

Re: [Freesurfer] mri_normalize problem normalization2

fer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_normalize problem normalization2 sure, send me the input to mri_normalize and I'll fix it On Wed, 28 Jun 2017, Chris Adamson wrote: > > Hello, > >   > > For one subject I’m getting a weird error on mri_normalize in n

Re: [Freesurfer] mri_normalize problem normalization2

sure, send me the input to mri_normalize and I'll fix it On Wed, 28 Jun 2017, Chris Adamson wrote: Hello,   For one subject I’m getting a weird error on mri_normalize in normalization2. When it goes into the “3d normalization pass 1 of 2” I get an error HISTOalloc(-2147383648): could not

[Freesurfer] mri_normalize problem normalization2

Hello, For one subject I'm getting a weird error on mri_normalize in normalization2. When it goes into the "3d normalization pass 1 of 2" I get an error HISTOalloc(-2147383648): could not allocate histogram The image that is produced by MRI3dGentleNormalize line 874 of

Re: [Freesurfer] Segmentation problem recon-all

curate because of dura left in the brainmask. cheers Bruce On Wed, 21 Jun 2017, Lisa Delalande wrote: Hi,   I am a PhD student and faced a problem with Freesurfer, more specially with segmentation. First of all,

Re: [Freesurfer] Segmentation problem recon-all

because of dura left in the > brainmask. > > cheers > Bruce > > On Wed, 21 Jun 2017, Lisa Delalande wrote: > > >> Hi, >> >> >> >> I am a PhD student and faced a problem with Freesurfer, more specially >> with >> segmentation. First of al

Re: [Freesurfer] Surface Problem

Can you send me your recon-all script to my email address (not to the list). I suspect it has been modified. On 06/21/2017 02:04 PM, Michael Davies wrote: > Hello, i have been trying to regenerate the surface on one of my > subjects but keep having a problem where the terminal is saying there

[Freesurfer] Surface Problem

Hello, i have been trying to regenerate the surface on one of my subjects but keep having a problem where the terminal is saying there is a missing file name. Do you have any suggestions please? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview

Re: [Freesurfer] Segmentation problem recon-all

wrote: Hi,   I am a PhD student and faced a problem with Freesurfer, more specially with segmentation. First of all, I did a typical qsub command. However, when I cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are often considered as grey matter. I tried these different

[Freesurfer] Segmentation problem recon-all

Hi, I am a PhD student and faced a problem with Freesurfer, more specially with segmentation. First of all, I did a typical qsub command. However, when I cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are often considered as grey matter. I tried these different commands

Re: [Freesurfer] lme_mass_RgGrow problem

Asunto: [Freesurfer] lme_mass_RgGrow problem Hello,We have been trying to analyze some longitudinal structural data using the FreeSurfer Mixed Effects Model toolbox and have been running into some issues. We have 2-3 timepoints per individual imaged across adolescence and 3 groups of interest. We

[Freesurfer] lme_mass_RgGrow problem

Hello, We have been trying to analyze some longitudinal structural data using the FreeSurfer Mixed Effects Model toolbox and have been running into some issues. We have 2-3 timepoints per individual imaged across adolescence and 3 groups of interest. We set up a design matrix to examine

[Freesurfer] pial problem and g-cut

dear freesurfer experts： I ran my subjects and i found there were lots of pial leave in the brainmask and affects the cortical surface, by following the troubleshooting tutorial i use the g-cut flag, the pial was cut while some brain matters were cut, too, and i found in my data fix the

Re: [Freesurfer] bbregister problem with --init-best

In those cases the cost of coreg is quite close to the optimal, for example, 0.366088 vs 0.366089. I guess the final results won't differ much if I used --init-coreg instead of --init-best. Best, Feilong On Fri, Mar 17, 2017 at 10:04 PM, Douglas Greve wrote: > what

Re: [Freesurfer] bbregister problem with --init-best

what happened in the ones that coreg was not the best? what is the nature of the data? On 3/17/17 6:39 PM, Feilong Ma wrote: Thanks, Doug! I've run bbregister with --init-best on my data comparing coreg, fsl, rr, and header; most of the times the choice is coreg as you said (59 out of 88

Re: [Freesurfer] bbregister problem with --init-best

Thanks, Doug! I've run bbregister with --init-best on my data comparing coreg, fsl, rr, and header; most of the times the choice is coreg as you said (59 out of 88 total runs). Best, Feilong On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve wrote: > Hi Feilong, you

Re: [Freesurfer] bbregister problem with --init-best

Hi Feilong, you do not need to use --init-best with bbregister anymore. It automatically uses --init-coreg (a remake of the spm coreg) which is the best as far a I can tell On 03/17/2017 02:47 PM, Feilong Ma wrote: > Hi FreeSurfer Developers, > > I'm having trouble using bbregister with the

Re: [Freesurfer] bbregister problem with --init-best

Awesome! Thanks for your help! Best, Feilong On Fri, Mar 17, 2017 at 2:57 PM, Z K wrote: > It seems that a freesurfer user just submitted a pull request yesterday > that fixes this bug: > > https://github.com/freesurfer/freesurfer/pull/24 > > Feel free to

Re: [Freesurfer] bbregister problem with --init-best

It seems that a freesurfer user just submitted a pull request yesterday that fixes this bug: https://github.com/freesurfer/freesurfer/pull/24 Feel free to download the fixed version: https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister On 03/17/2017 02:47 PM, Feilong

[Freesurfer] bbregister problem with --init-best

Hi FreeSurfer Developers, I'm having trouble using bbregister with the `--init-best` flag, a minimal example and error message is like this: $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta ERROR: cannot

Re: [Freesurfer] Freesurfer labeling problem?

Dear Reetta-Liina, Thanks for pointing out this inconsistency. The mapping is: GC-ML-DG = GC-DG CA3 = CA2/3 molecular_layer_HP = molecular layer Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com

Re: [Freesurfer] freeview problem with w-file overlay

sure, use save_mgh to write them to a .mgz or .mgh file cheers Bruce On Mon, 6 Feb 2017, Björn Herrmann wrote: Dear list, I would like to use freeview to display my activations patterns. I source-localized MEG data in matlab using the freesurfer standard brain as a source space. I saved

Re: [Freesurfer] freeview problem with w-file overlay

You can write it out as a curv (write_curv.m), or you can use mri_surf2surf to convert from w (aka paint) to curv or mgh format On 02/06/2017 01:33 PM, Björn Herrmann wrote: > Dear list, > > I would like to use freeview to display my activations patterns. I > source-localized MEG data in matlab

[Freesurfer] freeview problem with w-file overlay

Dear list, I would like to use freeview to display my activations patterns. I source-localized MEG data in matlab using the freesurfer standard brain as a source space. I saved the source localization as a w-file, that is, as an overlay. I used to display the overlay in tksurfer, but I cannot

Re: [Freesurfer] mri_label2label problem

Hi Doug, Yes i was visualising it on fsaverage. I switched to sub003 and the ROI looks perfect. What a simple mistake, thanks for your help. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031

Re: [Freesurfer] mri_label2label problem

Are you visualizing the output on subject sub003? It looks like fsaverage On 01/26/2017 06:23 PM, Bronwyn Overs wrote: > Hi Mailing list, > > I have been running the mri_label2label command and have encountered a > problem with the newly generated label. The command I am running is as >

Re: [Freesurfer] License problem

if recon-all works then you must have a license file. Are you sure that FREESURFER_HOME is defined in your environment and points to the right place? That's where we look for the license file (then in /Applications/freesurfer on the mac if FREESURFER_HOME isn't defined in the env0 cheers

Re: [Freesurfer] License problem

At the current stage I can run recon-all and get the results without problems. If the license would not work I couldn't be able to run it. Can someone send me the type of license file I should generate? In the website it says that I should get a license.txt by email, but I didn't get any file

Re: [Freesurfer] License problem

Is the file you created located in /Applications/freesurfer? Also, fir good measure, try creating the same file but naming it .license in the /Applications/freesurfer On 12/16/2016 11:20 AM, Marco Ganzetti wrote: > Dear all, > I am trying to display a volumetric file to a surface using

[Freesurfer] License problem

Dear all, I am trying to display a volumetric file to a surface using mri_vol2surf and then tksurfer. Here is the error message I get. I have obtained the email with the few license lines to copy in a file (that i created) name license.txt I created a new file and erased the existing LICENSE

Re: [Freesurfer] Build problem

gt; > Sent: Friday, December 2, 2016 4:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Build problem > > My guess is its a compatibility issue with the dependency package and > Fedora 23. Although I would have guessed it would have worked, the build

Re: [Freesurfer] Build problem

mber 2, 2016 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Build problem My guess is its a compatibility issue with the dependency package and Fedora 23. Although I would have guessed it would have worked, the build instructions have only been tested on Ubuntu, Debian and Ce

Re: [Freesurfer] Build problem

sable-Werror > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K > <zkauf...@nmr.mgh.harvard.edu> > Sent: Friday, December 2, 2016 4:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Bu

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