Hi Longchuan, when I asked for the terminal output, I meant the stuff that gets printed to the screen when the command runs. Try running it outside of your script to capture the output. Also, does the old program require 20G ? doug
On 08/27/2012 04:20 PM, Longchuan Li wrote:
Hi, Doug Here is the output from my log file and my command. I have been running this command many times and sometimes the job got killed, but sometimes they finished without error.
/usr/local/sge/bitc/spool/node13/job_scripts/77912: line 7: 30345 Killed /home/lli/freesurferv51/bin/mri_label2vol.linux --offset 1 --annot /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/label/rh.randomroi300_WithoutMedialWall.MacaqueYerkes6_to_RVJ8_Preuss_20111115.annot --temp /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/brain.mgz --subject RVJ8_Preuss_20111115 --hemi rh --fillthresh 0 --proj frac 0 0.5 0.05 --o /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/rh.randomroi300_WithoutMedialWall_Ribbon.MacaqueYerkes6_to_RVJ8_Preuss_20111115_fill0_projs0_proje0.5_projin0.05.nii.gz --identity
Many thanks in advance!
Longchuan
*From:* Douglas Greve greve@nmr.mgh.harvard.edu *To:* Longchuan Li leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, August 27, 2012 3:47 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What is your command line and what is the terminal output? doug
On 8/27/12 7:57 PM, Longchuan Li wrote:
Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
*From:* Leon leonado78@yahoo.com mailto:leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 3:48 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com mailto:leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 1:32 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *To:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
Hi, Douglas I have uploaded the file to the system. Also, my new results showed that when ic3.tri (instead of ic2.tri) is used as the input, one ROI at the similar location is also
missing.
Hope it will help you diagnose.
Thanks Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Sent:* Monday, June 4, 2012 1:00 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Can you upload the subject to our file drop system?
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
On 06/04/2012 12:24 PM, Leon wrote:
Hi, Douglas
Thank you very much for the updated one. I tested the new codes and the problem is still there. The ID for the original version that generates a mask with one missing ROI is:
$Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
I remember this is a version I downloaded from a link in FS
archive.
The ID for the one you sent to me is:
$Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
They look almost identical. Do you have any ideas what else may
cause
this issue and possible workaround?
Thank you
Leon
*From:* Douglas Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
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*Sent:* Friday, June 1, 2012 11:29 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What version are you using? I fix a problem last Sept that might be like this. I've put a new version of mri_label2vol here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
Try this and let me know if it works. doug
On 6/1/12 10:46 PM, Leon wrote:
Hi, Bruce Here are my two command lines For transferring the annot from the source template to the target subject:
/home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject} --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval src_2_trg.annot --hemi rh --surfreg sphere.reg0
Where sphere.reg0 is the registration from the target subject
to the
source subject.
For transfer them to the volume file:
/home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject}
--hemi
rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz --identity
Here is output for one of my transformations:
Setting mapmethod to nnf Source registration surface changed to sphere.reg0 Target registration surface changed to sphere.reg0 srcsubject = MacaqueA srcval = (null) srctype = trgsubject = MacaqueB trgval =
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
trgtype = srcsurfreg = sphere.reg0 trgsurfreg = sphere.reg0 srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0 Loading source data Reading surface file /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig reading colortable from annotation file... colortable with 162 entries read (originally /usr/local/freesurfer/lib/bem/ic2.tri) Reading target surface reg /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0 Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (61916)
Surf2Surf: Dividing by number of hits (61916) INFO: nSrcLost = 17467 nTrg121 = 61916, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910,
MnSrcMultiHits
= 0.920927 Saving target data Converting to target annot Saving to target annot
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
step2: writing the surface label to volume... Number of labels: 0 Annot File:
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
Template Volume: /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz Outut Volume:
/home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0.3 ProjStop: 0.8 ProjDelta: 0.05 Subject: MacaqueB Hemi: rh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $ Template RAS-to-Vox: -------- -1.000 -0.000 -0.000 160.000; -0.000 -0.000 -1.000 160.000; -0.000 1.000 -0.000 160.000; -0.000 -0.000 -0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 160.000; 0.000 0.000 -1.000 160.000; 0.000 1.000 0.000 160.000; 0.000 0.000 0.000 1.000; INFO: loading surface /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.white nvertices = 61916 Reading thickness /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.thickness Loading annotations from
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
reading colortable from annotation file... colortable with 162 entries read (originally /usr/local/freesurfer/lib/bem/ic2.tri) annotidmax = 162 Allocating Hit Volume (1013448704) voxels nlabels = 162
PVF (null) Thesholding hit volume. mri_label2vol done
*From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
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<mailto:fischl@nmr.mgh.harvard.edu
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<mailto:fischl@nmr.mgh.harvard.edu
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*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>>
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<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
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<mailto:freesurfer@nmr.mgh.harvard.edu
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<mailto:freesurfer@nmr.mgh.harvard.edu
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<mailto:freesurfer@nmr.mgh.harvard.edu
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*Sent:* Friday, June 1, 2012 8:02 PM *Subject:* Re: [Freesurfer] missing ROI when using
mri_label2vol to
transfer ic2.tri
Can you send us your command lines and screen output?
On Jun 1, 2012, at 7:44 PM, Leon <leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>>> wrote:
> Hi, folks > > when I transferred the annotation file obtained using > mri_make_face_parcellation based on ic2 (162 labels) to a volume > file using mri_label2vol, I found that one ROI patch was
missing in
> the volume file (see attached). I searched archives and the
closest
> thread I could found is that somebody reported an ROI with
the last
> index was missing in the mgz file after they were transferred
from
> the annotation file to the volume file. > > Could someone help on this? If this happens to be a bug, is there > any other strategy that will allow me to get a GM/WM ribbon
without
> a hole on it? > > Many thanks in advance > Leon > <MissingROI.jpg> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.