Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Tracula error - unknown queue "long.q", "short.q"
by Joana Braga Pereira 05 Sep '13

05 Sep '13

Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks!

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using mris_make_surfaces for nonstandard input
by David Romano 05 Sep '13

05 Sep '13

Hi everyone, I would like to produce lh.white, lh.area, and lh.curv files of the type produced by mris_make_surfaces, but where the input is a mask of the left hemisphere white matter alone. Specifically, suppose I start with the file lh.wm-mask.nii and use mri_convert to make lh.wm-mask.mgz. I can then follow the -tessellate and -fix steps of the -autorecon2 section on the webpage http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable to produce the file lh.orig, one of the required inputs to mris_make_surfaces. The only other files required to have mris_make_surfaces produce lh.white, lh.area, and lh.curv files, seem to be the files filled.mgz, brain.mgz, and wm.mgz. Since wm.mgz is the output of a call to mri_pretess from the -segmentation step of the -autorecon2 section, I can create wm.mgz by using the command mri_pretess lh.wm-mask.mgz 1 wm.mgz. My inclination at this point is to create copies of wm.mgz that are given the names filled.mgz and brain.mgz. I can then run mris_make_surfaces -whiteonly -noaparc -mgz subjectID lh and the desired files are produced, but I'm not sure what the effect of using wm.mgz as both filled.mgz and brain.mgz would have on the output. Given this setting, my question is: what are the roles played by filled.mgz an brain.mgz in creating the output of mris_make_surfaces? Thanks in advance for your help, David Romano

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Output mris_anatomical_stats into table for spreadsheet
by Tara Ann Miskovich 05 Sep '13

05 Sep '13

Hello everyone, I am trying to gather the curvature (of a frontal ROI created through mri_mergelabels) through mris_anatomical_stats using the following mris_anatomical_stats -l 1220/label/lh.frontalmerge.label -f frontal_table 1220 lh pial The table produced doesn't upload well into a spreadsheet (measurements all in one cell). Does anyone know how to make a table that can be uploaded into a spreadsheet? Thanks! Tara

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lh.orig.nofix vs. lh.white
by David Romano 05 Sep '13

05 Sep '13

Hi everyone, I've been trying to go through the various steps described on the page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I'm trying to understand part of the -autorecon2 section, and in particular, 1) how the lh.orig.nofix file that is produced by the end of the -tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and 2) whether the area and curvature files produced by the command

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Re: [Freesurfer] Improving the accuracy of average surfaces made from make_average_subject
by Bruce Fischl 05 Sep '13

05 Sep '13

Hi Miggy can you cc the list so that others can answer? The two atlases we provide are described in: https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/pdf/nihms213933.pdf and yes, I guess you could edit the ribbon.mgz and then convert it back to wm.mgz. You'll need to make sure that the "on" edits are turned to 255 and the "off" ones to 1 (not 0) for things to work properly cheers Bruce On Wed, 4 Sep 2013, Miggy Chuapoco wrote: > Hi Bruce, > Thanks for the help. To explain a bit more about the first issue, we convert > ribbon.mgz into a a nifti file using a script in matlab, which we then edit > in ITK-SNAP to fix the segmentation. Typically from there we use a program > called mrVista to create meshes and do other data analysis depending on what > we need to do. However, we are doing group averaging for the first time and > we would like to use these fixed segmentations that we have in the group > averaging, and not the raw segmentations from recon-all. I was curious to > know that if I were able to convert the nifti file that we have edited back > into an .mgz file, would we be able to theoretically obtain a new wm.mgz > file and run autorecon2-wm. Let me know if that makes sense. > > With regards to the second issue, which atlas is used in the > make_average_subject process and where would I be able to find a list of the > annotation files within each atlas? > > Thanks for your help! > Miggy > > > On Wed, Sep 4, 2013 at 1:45 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Miggy, > > not sure about your first issue as the ribbon is the gray matter > and the wm.mgz is white matter, so how would edits in one change > the other? > > For the second one, there is a flag in mris_register that allows > you to draw a label on an individual subject and indicate what > parcellation unit is should be in the average. The syntax is: > > > mris_register -l <label file> <gcsa file> <annotation name> ... > > where > > <label_file> is the label you draw on the individual (e.g. in > tksurfer) > <gcas_file> is one of our standard atlases, listed in > $FREESURFER_HOME/average/*.gcs > <annotation name> is the name of the annotation in the atlas > that the label should map to (e.g. S_central in the Destrieux > atlas) > > cheers > Bruce > > > On Wed, 4 Sep 2013, Miggy Chuapoco wrote: > > Hi all, > I'm trying to make a group average of a set of > subjects that we've collected > various functional data on and use anatomical > landmarks of the group average > surface to predict the locations of functional areas > that we've found to be > correlated to the anatomy of the ventral cortex. As > such, we'd like to get > as accurate of an average surface as possible. I've > come up on two problems > that I'd like to address and was wondering if anyone > could help come up with > a solution. > > I ran the recon-all command on all the subjects and > created a segmentation, > however we made edits to the segmentation using > ITK-SNAP, and not tkmedit. > Some of the changes were fairly drastic and we'd > like to use the fixed > segmentations in the averaging process. I've > considered perhaps running the > -autorecon2-wm flag, but unfortunately using > ITK-SNAP essentially makes > edits to ribbon.mgz, and not wm.mgz. I was wondering > if there was a way to > "extract" a new wm.mgz from an edited ribbon.mgz. > > My second problem involves trying to anchor a sulcus > on the ventral surface > during the averaging process (the mid-fusiform > sulcus) in hopes of getting a > more accurate representation of the sulcus on the > average surface. As it > stands there is a bit too much variability of the > average MFS location when > compared to the individual subjects' MFS location, > and we'd like to reduce > that if possible. Is there any way of using a label, > or something similar, > that can be considered as an "anchor" during the > averaging process? > > Thanks and regards, > Miggy Chuapoco > > > > > 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. > > > >

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license error with FS5.3
by S.V.Shepherd [work] 05 Sep '13

05 Sep '13

I wanted to bump this: I have license errors with FS 5.3 that don't appear for equivalently-configured FS 5.1 and FS 4.5 installations. How shall I troubleshoot? SYMPTOMS: $ mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz mri_convert /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz T1.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/.license -------------------------------------------------------------------------- $ bugr FREESURFER_HOME: /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 5.9 (Tikanga) Kernel info: Linux 2.6.18-308.4.1.el5 x86_64 LICENSE The license file is the same as we use for our other FS installations, which work. I've also tried copying it from .license to license, which didn't solve the problem. Please let me know if you have any leads or suggestions. *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

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Qdec Help
by Muhammad Naveed Iqbal Qureshi 05 Sep '13

05 Sep '13

Dear List Members, When I try to run the qdec I got following error, Please tell me how to rectify it. bmssa-desktop:~/freesurfer/subjects> qdec qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Thanks. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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qdec.table.dat help
by Muhammad Naveed Iqbal Qureshi 05 Sep '13

05 Sep '13

Dear list membes, Please guide me how to create the qdec.table.dat for my own mri data. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: R: Re: Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

Error: Parsing command line options Option -fmin not recognized This option was not recognized and ignored. ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 5-set-2013 1.40 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: R: Re: Mask from cortical parcellation use tkmedit Diff01 orig.mgz -overlay frontal_rh.nii.gz -fmin 0.5 On 09/04/2013 07:36 PM, stdp82(a)virgilio.it wrote: > When I use tkmedit Diff01 orig.mgz frontal_rh.nii.gz I have this error. > Error: Loading Surface frontal_rh.nii.gz > Couldn't load the surface. > Tkmedit couldn't read the surface you specified. This could be because > the file wasn't a surface type that tkmedit recognizes or the file was > unreadable due to permissions. > > I do not visualize the mask on T1, neither by tkmedit. It seem that > they have different dimension. > > thanks > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 5-set-2013 1.25 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Mask from > cortical parcellation > > The orientation looks right to me, ie, the little letters on the side > that indicate direction are correct. The odd orientation that it is > displayed in is an fslview issue > > > > On 09/04/2013 07:16 PM, stdp82(a)virgilio.it wrote: > > If I not change the output orientation the .nii.gz is wrong (please > > see attached file). > > > > mri_convert --in_type mgz --out_type nii T1.mgz T1.nii.gz > > > > > > ----Messaggio originale---- > > Da: greve(a)nmr.mgh.harvard.edu > > Data: 5-set-2013 1.09 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Mask from > > cortical parcellation > > > > Don't change the output orientation in mri_convert > > > > On 09/04/2013 07:05 PM, stdp82(a)virgilio.it wrote: > > > T1.mgz is corrected in tkmedit. > > > > > > When I added also frontal_rh.nii.gz > > > > > > tkmedit Diff01 orig.mgz frontal_rh.nii.gz > > > > > > Error: Loading Surface frontal_rh.nii.gz > > > Couldn't load the surface. > > > Tkmedit couldn't read the surface you specified. This could be because > > > the file wasn't a surface type that tkmedit recognizes or the file was > > > unreadable due to permissions. > > > > > > This is the command lines that I used for mri_binarize: > > > mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1018 1019 1020 > > > 1026 1027 1028 1032 --o frontal_rh.nii.gz > > > > > > and for mri_convert: > > > mri_convert --in_type mgz --out_type nii --out_orientation RAS T1.mgz > > > T1.nii.gz > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > ----Messaggio originale---- > > > Da: greve(a)nmr.mgh.harvard.edu > > > Data: 5-set-2013 0.49 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Mask from cortical > > > parcellation > > > > > > > > > first, display it in tkmedit and verify that it is incorrect there. If > > > it is correct, then the problem is in your viewer > > > If it is incorrect, send me the command lines you used for mri_binarize > > > and mri_convert > > > > > > > > > On 09/04/2013 06:46 PM, stdp82(a)virgilio.it wrote: > > > > I have used mri_convert to obtain T1.nii.gz from T1.mgz. > > > > I attached the image that shows what's happened when I have overlayed > > > > the frontal mask (obtained by mri_binarize) on T1.nii.gz. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: greve(a)nmr.mgh.harvard.edu > > > > Data: 5-set-2013 0.07 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: Re: R: R: Re: Mask from cortical parcellation > > > > > > > > > > > > use the orig.mgz or any of the other FS volumes > > > > > > > > On 09/04/2013 05:48 PM, stdp82(a)virgilio.it wrote: > > > > > > > > > > I'd like to perform probtrackx (FSL) from seed (subcortical) to > > target > > > > > (cortical) masks. > > > > > > > > > > To this aim, I should trasform all cortical and subcortical masks > > > > > obtained by FS on MNI space. > > > > > > > > > > Therefore, firstly, I'd like to overlay the masks that I > > obtained by > > > > > mri_binarize on the structural image to check the masks. > > > > > > > > > > Next, I'd like to apply FLIRT to trasform all masks in a common > > > > > MNI152_1mm space. > > > > > > > > > > My problem is " which is the T1.nii.gz that can I use to overlay the > > > > > cortical masks created by mri_binarize?" > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: greve(a)nmr.mgh.harvard.edu > > > > > Data: 4-set-2013 23.28 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] R: R: Re: Mask from cortical parcellation > > > > > > > > > > I don't understand your question. Can you elaborate? > > > > > On 09/04/2013 05:27 PM, stdp82(a)virgilio.it wrote: > > > > > > I mean anatomical.nii.gz with the same spatial features of the > > > masks. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: stdp82(a)virgilio.it > > > > > > Data: 4-set-2013 23.02 > > > > > > A: <greve(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: [Freesurfer] R: Re: Mask from cortical parcellation > > > > > > > > > > > > Thank you very much. > > > > > > > > > > > > A last help, please. How is the anatomical file that I can use to > > > > > > overlay the masks. I'm noting that masks are characterized by: > > > > > > data_type INT32 > > > > > > dim1 256 > > > > > > dim2 256 > > > > > > dim3 256 > > > > > > dim4 1 > > > > > > datatype 8 > > > > > > pixdim1 1.0000000000 > > > > > > pixdim2 1.0000000000 > > > > > > pixdim3 1.0000000000 > > > > > > pixdim4 0.0109999999 > > > > > > cal_max 0.0000 > > > > > > cal_min 0.0000 > > > > > > file_type NIFTI-1+ > > > > > > > > > > > > Regards, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: greve(a)nmr.mgh.harvard.edu > > > > > > Data: 4-set-2013 17.10 > > > > > > A: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: [Freesurfer] Mask from cortical parcellation > > > > > > > > > > > > > > > > > > > > > > > > you can use mri_binarize on aparc+aseg, eg, something like > > > > > > > > > > > > mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o > > > > > > frontal.nii.gz > > > > > > > > > > > > those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > > > That table has a lot of ROIs in it, and not all will be in the > > > > > > aparc+aseg. You'll be interested in the ones between 1000-1035 and > > > > > > 2000-2035 > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 09/04/2013 08:46 AM, stdp82(a)virgilio.it wrote: > > > > > > > Hi list, > > > > > > > > > > > > > > I need to create a mask of frontal, parietal, temporal and > > > occipital > > > > > > > lobes in a subject by using cortical parcellation output. > > > > > > > > > > > > > > Is it possible? Eventually, how can I transform these masks > > > file to > > > > > > > mii.gz (to import them in FSL analysis). > > > > > > > > > > > > > > Thank you very much. > > > > > > > > > > > > > > Regards, > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > > > > Douglas N. Greve, Ph.D. > > > > > > MGH-NMR Center > > > > > > greve(a)nmr.mgh.harvard.edu > > > > > > Phone Number: 617-724-2358 > > > > > > Fax: 617-726-7422 > > > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > -- > > > > Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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error during longitudinal -base stream
by Rongxiang Tang 04 Sep '13

04 Sep '13

Hi All, I found an error during the longitudinal -base stream: #@# Ex-vivo Entorhinal Cortex Label lh Wed Sep 4 19:35:00 CDT 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject 611. processing subject lh.EC_average... MRISread(/mnt/fs1/work/results/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /mnt/fs1/work/results/lh.EC_average/surf/lh.sphere.reg Not a directory mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label 611 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /mnt/fs1/work/results/611/mri/wm.mgz... reading input surface /mnt/fs1/work/results/611/surf/lh.white... reading input pial surface /mnt/fs1/work/results/611/surf/lh.pial... reading input white surface /mnt/fs1/work/results/611/surf/lh.white... INFO: assuming MGZ format for volumes. No such file or directory mris_anatomical_stats: could not open label file ./lh.entorhinal_exvivo.label No such file or directory 611: could not read label file (null) No such file or directory #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Sep 4 19:35:05 CDT 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject 611. processing subject rh.EC_average... MRISread(/mnt/fs1/work/results/rh.EC_average/surf/rh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /mnt/fs1/results/rh.EC_average/surf/rh.sphere.reg Not a directory mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label 611 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /mnt/fs1/work/results/611/mri/wm.mgz... reading input surface /mnt/fs1/work/results/611/surf/rh.white... reading input pial surface /mnt/fs1/work/results/611/surf/rh.pial... reading input white surface /mnt/fs1/work/results/611/surf/rh.white... INFO: assuming MGZ format for volumes. No such file or directory mris_anatomical_stats: could not open label file ./rh.entorhinal_exvivo.label No such file or directory 611: could not read label file (null) No such file or directory #------------------------------------------ Started at Wed Sep 4 10:22:15 CDT 2013 Ended at Wed Sep 4 19:35:10 CDT 2013 #@#%# recon-all-run-time-hours 9.215 recon-all -s 611 finished without error at Wed Sep 4 19:35:10 CDT 2013 done although it tells me that the subject finished without error, clearly there is some error....does it affect my analysis or could I simply ignore it? Thanks in advance, Catherine

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