My apologies - there was a typo in my last message. The error reads that the
program could not find mri/001.mgz:
cibsr-i27-410:inProgress6.0b kel32$ pwd
/Volumes/Xspace/Freesurfer/inProgress6.0b
cibsr-i27-410:inProgress6.0b kel32$ ls
18512_T1_v5.3_hipp_v6.0 18512_hipp fsaverage
cibsr-i27-410:inProgress6.0b kel32$ recon-all -all -s 18512_T1_v5.3_hipp_v6.0
-hippocampal-subfields-T2
/Volumes/Xspace/Freesurfer/Liraglutide6.0b/rawdata/18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm
T2hipp_in_long
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-OSX-dev-20160326
INFO: SUBJECTS_DIR is /Volumes/Xspace/Freesurfer/inProgress6.0b
Actual FREESURFER_HOME /Volumes/ToolsMac/freesurfer6.0b
-rw-rw-r-- 1 kel32 staff 1368492 Apr 26 08:33
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log
Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar
18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main executable
(/usr/bin/top) is setuid or setgid
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Volumes/ToolsMac/freesurfer6.0b
Previous: /Volumes/ToolsMac/freesurfer5.3
#--------------------------------------------
#@# MotionCor Tue Apr 26 08:41:07 PDT 2016
ERROR: no run data found in
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri. Make
sure to
have a volume called 001.mgz in
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar
18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
recon-all -s 18512_T1_v5.3_hipp_v6.0 exited with ERRORS at Tue Apr 26 08:41:08
PDT 2016
For more details, see the log file
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Can you please advise on how best to proceed?
May thanks!
Lara
Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter
<mreu...@nmr.mgh.harvard.edu>
Sent: Tuesday, April 26, 2016 6:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans
prior to analysis
Hi Lara,
mri/orig.mgz should be there also in the longitudinal directories. If it
is missing, more might be wrong. I would recommend rerunning those long
runs from scratch.
Best, Martin
On 04/25/2016 07:07 PM, Lara Foland-Ross wrote:
> Thank you Eugenio! This worked like a charm.
>
> Wondering now if you could help me troubleshoot running this command on 2
> scans from a single subject (time 1 and time 2) that were processed using the
> longitudinal pipeline in version 5.3.
>
> I ran the following:
>
> recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2
> 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm
> T2hipp
>
> and got the error that Freesurfer could not find mri/orig file... It is
> indeed not there, presumably because it isn't produced after the creation and
> editing of the long.base timepoints. I read elsewhere on the list that the
> hippocampal subfield analysis could be run on the individual longitudinal
> timepoints but can't seem to get this to work. Can you advise?
>
> Many thanks in advance for your continued help!
> Lara
>
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias
> <e.igles...@bcbl.eu>
> Sent: Tuesday, April 5, 2016 3:59 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two
> scans prior to analysis
>
> Almost correct!
> recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2
> subj1_hipp/I0001.dcm T2hipp
> Also, this is assuming that you have defined the environment variable
> SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd <subjectsDirectory>.
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> ----- Original Message -----
> From: "Lara Foland-Ross" <lfol...@stanford.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Wednesday, April 6, 2016 12:29:09 AM
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two
> scans prior to analysis
>
> Hi Eugenio,
>
> Thank you so much for the quick and helpful reply. I checked the images in
> Freeview and they actually line up quite nicely!
>
> Can you provide further guidance on how to run recon-all once with both the
> -all and the hippocampal-subfields-T1T2 flags?
>
> For example, in my rawdata directory, I have two folders: subj1_T1 and
> subj1_hipp. I cd'd into the rawdata folder and ran the following with no
> success:
>
> recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2
> subj1_hipp T2hipp
>
> Is this directory setup correct? And can you please point out the errors in
> the above recon-all command?
>
> Many thanks again for your help!
> Lara
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias
> <e.igles...@bcbl.eu>
> Sent: Tuesday, April 5, 2016 2:32 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two
> scans prior to analysis
>
> Dear Lara,
> Two things:
> 1. You don't need to recon the T2 scan. The recon-all stream only works for
> T1 data anyway.
> 2. The registration between the T1 and T2 scans happens internally (with a
> mri_register command similar to the one you wrote) during the hippocampal
> subfield segmentation. You only need to coarsely align the T1 and T2 scans
> manually if the initial alignment between the two is terrible. What happens
> when you open them both in Freeview?
> 3. If the alignment is decent, just run recon-all once, with both the -all
> and the -hippocampal-subfields-T1T2 flags.
> Feel free to send me the T1 and T2 scans if you are not sure whether they are
> sufficiently well aligned or not.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> ----- Original Message -----
> From: "Lara Foland-Ross" <lfol...@stanford.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Tuesday, April 5, 2016 11:14:39 PM
> Subject: [Freesurfer] hippocampal subfield analysis - registered two scans
> prior to analysis
>
> Hello,
>
> I'm beginning a hippocampal subfield analysis in the beta version of
> Freesurfer 6.0. I have a whole brain T1-weighted image as well as a
> high-resolution T2-weighted image of the hippocampus. The T2 weighted image
> covers the entire hippocampus, but not the whole brain.
>
> My understanding (and please correct me if I'm wrong) is that I should first
> run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted
> scan using the -hippocampal-subfields-T1T2 flag, but that I must first make
> sure that the two scans are roughly aligned.
>
> I was able to successfully register the T1-weighted scan to the T2-weighted
> scan using mri_robust_register using the following commands:
>
> mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi
> --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
>
> mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz
> wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
>
> My plan was then to run recon-all on the newly upsampled, registered
> wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the
> T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the
> resampled whole brain T1-weighted image now has only a partial FOV.
>
> Is there a way that I can preserve the full field of view in the T1-weighted
> scan? I've experimented with mri_coreg and flirt and am at a loss.
>
> Many thanks in advance,
> Lara
>
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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>
>
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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