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

Gesendet: Freitag, 13. Januar 2023 16:27:17 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution -i needs to be followed by the input volume Move /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz r

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

, 2023 9:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found * External Email - Caution * External Email - Use Caution Hey again, sorry for my many problems, but this did not work as well (same error) $ recon-all -s sub-04 -i

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

On Behalf Of Livia Ruehr Sent: Friday, January 13, 2023 9:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Hello, I've tried the echo command, which didn't work. Afterwards I tried -sd:

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

. Januar 2023 15:30:51 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found Hi Livia, I’m not sure why your $SUBJECTS_DIR is not recognized. In the same terminal window, 1. echo $SUBJECTS_DIR 2. submit your recon-all If this doesn’t work, you can u

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

Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Livia Ruehr Sent: Friday, January 13, 2023 7:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Hi, I've tried it today

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

_ Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Huang, Yujing Gesendet: Donnerstag, 12. Januar 2023 18:25:58 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found Hi Livia, Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.g

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

: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Dear Yujing, Thank your for your fast reply. So you mean that I need to paste the whole path (home/../../..) before the name of the .nii.gz file in the comm

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

are there on this level without any subdirectories...? Best Livia Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Huang, Yujing Gesendet: Donnerstag, 12. Januar 2023 17:53:41 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all

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

Hi Livia, SUBJECTS_DIR is the root directory for recon-all processed data. Each individual subject will have a separate subdirectory under SUBJECTS_DIR. You need to specify full path to your images in recon-all command line. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behal

Re: [Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Try: export TUTORIAL_DATA=/home/shao/tutorial_data Tim > On August 11, 2020 at 6:51 AM Wei Shao wrote: > > > External Email - Use Caution > > Hi, Freesurfer Team > > My name is Wei Shao, I just a beginner of Freesurfer. As I play

[Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it alway

Re: [Freesurfer] Problem with Recon-All for Volmetric

you mean not to generate surfaces/parcellations/thickness? I guess you could run -autorecon1 -autorecon2. That would do the start of the surface stuff, but not much (and not long) cheers Bruce On Tue, 30 May 2017, Becker, Valerie wrote: Hi all, Forgive me, as I' new at this, but I cant s

Re: [Freesurfer] Problem with Recon-All for Volmetric

you can run it with -autorecon1 -autorecon2 On 05/30/2017 04:00 PM, Becker, Valerie wrote: > > Hi all, > > > Forgive me, as I' new at this, but I cant seem to quite make heads or > tails of the Recon-all page with instructions on how to divide it the > commands. We're just trying to run indivi

[Freesurfer] Problem with Recon-All for Volmetric

Hi all, Forgive me, as I' new at this, but I cant seem to quite make heads or tails of the Recon-all page with instructions on how to divide it the commands. We're just trying to run individual volumetric analyses at the moment. Is there a way to do that with a recon- proc? So as to shorten pr

Re: [Freesurfer] Problem with recon-all

Hi Mads yes, you should be able to use mri_convert to change it to .mgz format and name it brainmask.mgz, after which I think it will look as if you've manually edited it and it will be applied cheers Bruce On Mon, 12 Oct 2015, Mads Jensen wrote: > I got a skullstrippen mask from another pipe

Re: [Freesurfer] Problem with recon-all

I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii thanks, mads On 5 October 2015 at 23:11, Andre van der Kouwe wrote: > I think the standard MP2RAGE only generates the T1 image on the scann

Re: [Freesurfer] Problem with recon-all

I think the standard MP2RAGE only generates the T1 image on the scanner. With the Bloch simulation you can also figure out PD but the online image analysis doesn't do it. On 10/05/2015 04:21 PM, Bruce Fischl wrote: > I thought mp2rage lets you derive a proton-density (PD) weighted image, > but I

Re: [Freesurfer] Problem with recon-all

I thought mp2rage lets you derive a proton-density (PD) weighted image, but I could be wrong. I'll cc Andre van der Kouwe who will know On Mon, 5 Oct 2015, Mads Jensen wrote: > Hi and thanks for the fast reply. > > Pardon my ignorance, but I am not sure that the PD images are? > > thanks, > mad

Re: [Freesurfer] Problem with recon-all

Hi and thanks for the fast reply. Pardon my ignorance, but I am not sure that the PD images are? thanks, mads On 5 October 2015 at 21:59, Bruce Fischl wrote: > Hi Mads > > my guess is that this is a problem with the MP2RAGE. We don't see this in > the mprage or memprage. Can you look at the PD

Re: [Freesurfer] Problem with recon-all

Hi Mads my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage cheers Bruce On Mon, 5 Oct 2015, Mads Je

[Freesurfer] Problem with recon-all

Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon ind

[Freesurfer] Problem with recon-all - nu_currect

Dear FS experts, I have a problem with the command "recon-all". In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command "nu_currect", as you can see from the file.log in a

[Freesurfer] Problem with recon-all

Dear FS experts, I have a problem with the command "recon-all". In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command "nu_currect", as you can see from the file.log in att

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

Dear Bruce, I have tried running mri_ca_register again twice with the following cases: Case 1: on VirtualBox with 9.2GB available free disk space. I gave 1GB RAM to this Virtual Machine. Case 2: on Ubuntu installed on a machine with 2 core Dual 2.5Ghz , 4G RAM, and 6GB free disk space. In

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

Hi Long, have you run out of disk space? Bruce On Tue, 24 Nov 2009, L wrote: > Dear Freesurfers, > > I have had a problem when running recon-all on your tutorial data (bert). > Please find following the content of recon-all.log: > > *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* > >

[Freesurfer] Problem with recon-all on the tutorial data (bert)

Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $* *MRISread(../surf/lh.inflat

[Freesurfer] problem with recon-all

hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all.  If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything.  here is the output from "recon-all-nmr

Re: [Freesurfer] problem with recon-all

I modified recon-all to try to autodetect the input format (but introduced a bug). It should work if you add -COR to the command-line. In the mean time I'll fix my mistake. doug Tamara Knutsen wrote: when i source: Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME /usr/loca

[Freesurfer] problem with recon-all

when i source: Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast SUBJECTS_DIR/space/sake/3/users/inverse/subjects FUNCTIONALS_DIR /usr/local/freesurfer/dev/sessions MINC_BIN_DIR/usr/pubsw/packages/mni/cu