[Freesurfer] (no subject)
nbsp; phi ,I have solved the the probelm./ppNow, I have some new question, just as belows:/pp1nbsp; In the GUI interface, I can't type the letters ,I don't know why?/pp2 when I choose the volume in the Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment./pp3 In the terminal command window, I type the make_average_subject command,It runs errors , show as :/pplimit:decriptors:can't remove limite(operation not permition), how to deal with this bug?/ppThank you very much!!!/ppnbsp;/p___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
nbsp; phi ,I have solved the the probelm./ppNow, I have some new question, just as belows:/pp1nbsp; In the GUI interface, I can't type the letters ,I don't know why?/pp2 when I choose the volume in the Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment./pp3 In the terminal command window, I type the make_average_subject command,It runs errors , show as :/pplimit:decriptors:can't remove limite(operation not permition), how to deal with this bug?/ppThank you very much!!!/pattachment: qdec_volume_error.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 scans vertical..x10 repetitions... Jonathan Polimeni schrieb: hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 3D volume generation, ROI selection, subvolume analysis
Good morning, We have been working on Slicer and have been able to read in our stack of images. I can view them at the desired cross-sections by moving the three planes at will. But now we would like to be able to generate a 3D volume (in this case a rectangular prism) that contains all of these images in the stack. Once this is assembled, we are interested in being able to have Slicer/Free Surfer select ROI's or do so ourselves and be able to analyze these subvolumes from within the prism itself. Before I delve to deeply into FreeSurfer, I just wanted to make sure that it was capable of providing these capabilities and that Slicer cannot do them on its own. Are there any resources that I could access to aid me that are not accessible through the main FreeSurfer site: http://surfer.nmr.mgh.hardvard.edu/fswiki ? Could you give me a few quick pointers to get me started? Thanks a lot. Greg _ Picture this – share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHMloc=us ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] problem to save images
Hello, group I have problems to save the display in TKsurfer. I tried 'Save RGB as', but I could not open the file with photoshop in windows, and it was total black when I opened it with adobe illustrator in windows or GIMP in Linux. Please tell me how to save the images so that I can open them with photoshop. Thank you in advance, XIn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Making labels from the commandline
Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2surf projection? I would want to set a threshold and have anything above that threshold be made into a label for that surface. Cheers, -Morgan Doug Greve wrote: I have a relatively new program that does this. Actually, it is an old program with a cryptic name (mri_cor2label). I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have been using mri_vol2surf to project nifti volumes onto subject surfaces but I am not sure I understand how to then convert the ouput .mgh file into a label that can then be used to sample the surface measures of that subject. I have attached an image of one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the surface. As you can see it contains perhaps three patches that I would like to treat as one label with which I could then use to sample the surface measures of the subject. Is this something I can do with mri_vol2surf? If I draw three labels on that subjects' surface, how do you then merge those labels together to be able to sample from the combined area? I have tried mri_mergelabel but I get a tail error when I try this: mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o lh.combo-it.label tail: cannot open `+3' for reading: No such file or directory tail: cannot open `+3' for reading: No such file or directory Done Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, what format is your volume ROI in? I think Doug's mri_vol2surf will do this. If you have it in our label format file, then just loading it into tksurfer will work if all the vertex #s are -1 (it will sample it onto the surface) Bruce On Thu, 24 May 2007, Morgan Hough wrote: I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem to save images
The RGB format is an old Irix format, I think. The UNIX/Linux program 'convert' should be able to convert it to a jpeg for you. On Wed, Jun 27, 2007 at 12:34:44PM -0400, Wang, Xin wrote: Hello, group I have problems to save the display in TKsurfer. I tried 'Save RGB as', but I could not open the file with photoshop in windows, and it was total black when I opened it with adobe illustrator in windows or GIMP in Linux. Please tell me how to save the images so that I can open them with photoshop. Thank you in advance, XIn -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Making labels from the commandline
Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2surf projection? I would want to set a threshold and have anything above that threshold be made into a label for that surface. Cheers, -Morgan Doug Greve wrote: I have a relatively new program that does this. Actually, it is an old program with a cryptic name (mri_cor2label). I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have been using mri_vol2surf to project nifti volumes onto subject surfaces but I am not sure I understand how to then convert the ouput .mgh file into a label that can then be used to sample the surface measures of that subject. I have attached an image of one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the surface. As you can see it contains perhaps three patches that I would like to treat as one label with which I could then use to sample the surface measures of the subject. Is this something I can do with mri_vol2surf? If I draw three labels on that subjects' surface, how do you then merge those labels together to be able to sample from the combined area? I have tried mri_mergelabel but I get a tail error when I try this: mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o lh.combo-it.label tail: cannot open `+3' for reading: No such file or directory tail: cannot open `+3' for reading: No such file or directory Done Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, what format is your volume ROI in? I think Doug's mri_vol2surf will do this. If you have it in our label format file, then just loading it into tksurfer will work if all the vertex #s are -1 (it will sample it onto the surface) Bruce On Thu, 24 May 2007, Morgan Hough wrote: I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Making labels from the commandline
Hi Doug, Thanks for the ftp fix. I have downloaded these fine now. I don't see a use case for making a label in mri_binarize's help. When I project the volumes to surfaces I actually save them as nifti files so I can keep using avwmaths++ when I want to. What I think I am missing now is the way to make that into a label file that I can then use to constrain mris_anatomical_stats to a particular patch of the cortical ribbon. Can mri_binarize produce such a file? Is there something I can feed its output into that would accomplish that? Cheers, -Morgan Doug Greve wrote: Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2surf projection? I would want to set a threshold and have anything above that threshold be made into a label for that surface. Cheers, -Morgan Doug Greve wrote: I have a relatively new program that does this. Actually, it is an old program with a cryptic name (mri_cor2label). I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have been using mri_vol2surf to project nifti volumes onto subject surfaces but I am not sure I understand how to then convert the ouput .mgh file into a label that can then be used to sample the surface measures of that subject. I have attached an image of one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the surface. As you can see it contains perhaps three patches that I would like to treat as one label with which I could then use to sample the surface measures of the subject. Is this something I can do with mri_vol2surf? If I draw three labels on that subjects' surface, how do you then merge those labels together to be able to sample from the combined area? I have tried mri_mergelabel but I get a tail error when I try this: mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o lh.combo-it.label tail: cannot open `+3' for reading: No such file or directory tail: cannot open `+3' for reading: No such file or directory Done Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, what format is your volume ROI in? I think Doug's mri_vol2surf will do this. If you have it in our label format file, then just loading it into tksurfer will work if all the vertex #s are -1 (it will sample it onto the surface) Bruce On Thu, 24 May 2007, Morgan Hough wrote: I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Making labels from the commandline
No, use mri_cor2label to create the label file. I think the 2nd example matches what you want to do. doug Morgan Hough wrote: Hi Doug, Thanks for the ftp fix. I have downloaded these fine now. I don't see a use case for making a label in mri_binarize's help. When I project the volumes to surfaces I actually save them as nifti files so I can keep using avwmaths++ when I want to. What I think I am missing now is the way to make that into a label file that I can then use to constrain mris_anatomical_stats to a particular patch of the cortical ribbon. Can mri_binarize produce such a file? Is there something I can feed its output into that would accomplish that? Cheers, -Morgan Doug Greve wrote: Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2surf projection? I would want to set a threshold and have anything above that threshold be made into a label for that surface. Cheers, -Morgan Doug Greve wrote: I have a relatively new program that does this. Actually, it is an old program with a cryptic name (mri_cor2label). I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have been using mri_vol2surf to project nifti volumes onto subject surfaces but I am not sure I understand how to then convert the ouput .mgh file into a label that can then be used to sample the surface measures of that subject. I have attached an image of one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the surface. As you can see it contains perhaps three patches that I would like to treat as one label with which I could then use to sample the surface measures of the subject. Is this something I can do with mri_vol2surf? If I draw three labels on that subjects' surface, how do you then merge those labels together to be able to sample from the combined area? I have tried mri_mergelabel but I get a tail error when I try this: mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o lh.combo-it.label tail: cannot open `+3' for reading: No such file or directory tail: cannot open `+3' for reading: No such file or directory Done Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, what format is your volume ROI in? I think Doug's mri_vol2surf will do this. If you have it in our label format file, then just loading it into tksurfer will work if all the vertex #s are -1 (it will sample it onto the surface) Bruce On Thu, 24 May 2007, Morgan Hough wrote: I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Making labels from the commandline
Hi Doug, I see what you mean now. mri_cor2label should do it. Thanks again. Cheers, -Morgan Doug Greve wrote: No, use mri_cor2label to create the label file. I think the 2nd example matches what you want to do. doug Morgan Hough wrote: Hi Doug, Thanks for the ftp fix. I have downloaded these fine now. I don't see a use case for making a label in mri_binarize's help. When I project the volumes to surfaces I actually save them as nifti files so I can keep using avwmaths++ when I want to. What I think I am missing now is the way to make that into a label file that I can then use to constrain mris_anatomical_stats to a particular patch of the cortical ribbon. Can mri_binarize produce such a file? Is there something I can feed its output into that would accomplish that? Cheers, -Morgan Doug Greve wrote: Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2surf projection? I would want to set a threshold and have anything above that threshold be made into a label for that surface. Cheers, -Morgan Doug Greve wrote: I have a relatively new program that does this. Actually, it is an old program with a cryptic name (mri_cor2label). I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have been using mri_vol2surf to project nifti volumes onto subject surfaces but I am not sure I understand how to then convert the ouput .mgh file into a label that can then be used to sample the surface measures of that subject. I have attached an image of one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the surface. As you can see it contains perhaps three patches that I would like to treat as one label with which I could then use to sample the surface measures of the subject. Is this something I can do with mri_vol2surf? If I draw three labels on that subjects' surface, how do you then merge those labels together to be able to sample from the combined area? I have tried mri_mergelabel but I get a tail error when I try this: mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o lh.combo-it.label tail: cannot open `+3' for reading: No such file or directory tail: cannot open `+3' for reading: No such file or directory Done Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, what format is your volume ROI in? I think Doug's mri_vol2surf will do this. If you have it in our label format file, then just loading it into tksurfer will work if all the vertex #s are -1 (it will sample it onto the surface) Bruce On Thu, 24 May 2007, Morgan Hough wrote: I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] OASIS Freesurfer Data
Hi folks- The Freesurfer processing of the OASIS cross-sectional data set is now available for download via anonymous FTP. The whole set will also be available at the OASIS website in the coming weeks. Check out www.oasis-brains.org for more information on the OASIS project. Download instructions: -ftp to www.oasis-brains.org -login as anonymous (use email address as password) -cd to data -mget oasis_cs_freesurfer* The full set is ~150 GB. It is divided into 11 separate .tar.gz files. This data set falls under the same Data Usage Agreement as the core OASIS data (http://www.oasis-brains.org/app/template/UsageAgreement.vm). Most importantly, please make sure to properly acknowledge its origin. Again, thanks to Bruce, Jenni, and the rest of the folks at MGH for generating this very cool data set and for making it widely available. Dan Marcus [EMAIL PROTECTED] Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average-subject
Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t make_average_surface input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz INFO: extension is mgz [EMAIL PROTECTED] Making rh annotation - Wed Jun 27 18:06:47 PDT 2007 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.curvature.buckner40.filled.desikan_killiany.gcs reading color table from GCSA file average std = 35.0 0.3 using min determinant for regularization = 0.011 0 singular and 829 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 376 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.atlas2005_simple.gcs reading color table from GCSA file average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... [EMAIL PROTECTED] Making average rh.orig surface - Wed Jun 27 18:07:06 PDT 2007 /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mris_make_average_surface -i 7 -o orig -sdir-out /space/emc1/3/data/TOP/Containers rh orig_avg sphere.reg/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest reading vertex positions from orig... mris_make_average_surface [options] hemi outsurfname cansurfname outsubject subj1 subj2 subj3 ... Run with -help for more info -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average-subject
Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t make_average_surface input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz INFO: extension is mgz [EMAIL PROTECTED] Making rh annotation - Wed Jun 27 18:06:47 PDT 2007 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.curvature.buckner40.filled.desikan_killiany.gcs reading color table from GCSA file average std = 35.0 0.3 using min determinant for regularization = 0.011 0 singular and 829 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 376 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.atlas2005_simple.gcs reading color table from GCSA file average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... [EMAIL PROTECTED] Making average rh.orig surface - Wed Jun 27 18:07:06 PDT 2007 /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mris_make_average_surface -i 7 -o orig -sdir-out /space/emc1/3/data/TOP/Containers rh orig_avg sphere.reg/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest reading vertex positions from orig... mris_make_average_surface [options] hemi outsurfname cansurfname outsubject subj1 subj2 subj3 ... Run with -help for more info ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
