Re: [Freesurfer] Pial surface errors
Hi Alex, it depends what the cause is. I think the most common is either bias field or intrinsic tissue variations. These can be fixed if the white matter at the base of the strand isn't intensity normalized, that is, if it has a value <110 in the T1 image. If that's the case, you can add some control points in the wm in these regions and rerun things. cheers, Bruce On Wed, 28 Sep 2005, Fornito, Alexander wrote: Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if there are any rules that might be useful to this end, or whether there is an alternative to fixing this problem? Thanks, Alex ___ 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
[Freesurfer] Pial surface errors
Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if there are any rules that might be useful to this end, or whether there is an alternative to fixing this problem? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mris_sample_parc
Hi Satra, that's what it does by default. cheers, Bruce On Tue, 27 Sep 2005, Satrajit Ghosh wrote: Hi, I'm trying to create an annotation file from a volume is mris_sample_parc. Is there any way to have it resample at 0.5 the distance between the white and pial surfaces? Thanks Satra ___ 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
[Freesurfer] Mris_sample_parc
Hi, I'm trying to create an annotation file from a volume is mris_sample_parc. Is there any way to have it resample at 0.5 the distance between the white and pial surfaces? Thanks Satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Freesurfer Digest, Vol 19, Issue 49
Blaise (and Keith), I was able to recreate the problem that Keith is seeing using a sample dicom file he sent, so I am working to resolve that issue. It seems to be a Mac-centric issue, as the same dicom will convert correctly on Linux. The odd thing is that the siemens_dicom files output from our scanner at MGH seem to convert correctly on the Mac using mri_convert, so that is one aspect to this problem that we are looking at (differences in formating). We use the Syngo sw on the scanner workstations. Can you also send me one of the dcm files that is failing for you? Its helpful to have multiple failure cases to test against. Thanks. Nick On Tue, 2005-09-27 at 15:34 -0400, Blaise Frederick wrote: > > On Sep 27, 2005, at 3:06 PM, [EMAIL PROTECTED] > wrote: > > > > > > Message: 2 > > Date: Tue, 27 Sep 2005 13:42:02 -0400 > > From: Keith Schneider <[EMAIL PROTECTED]> > > Subject: [Freesurfer] mri_convert doesn't recognize DICOM files > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: > > <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > > > > I installed Freesurfer on a G5 Tiger Mac, but mri_convert and  > > mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a  > > Siemens Trio 3T) as DICOM files. Has anyone else encountered this? > > > > > > Other programs can read the DICOM files just fine. > > > > > > keith > > > > > > > > > > -- > > > I have found exactly the same thing. The thing is, it _used_ to > work... > > > Using a G5 with 10.4.2, in a directory with DICOM files pulled off a > Siemens Trio using Osirix, I execute the following: > > > /usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze > IM-0242-0001.dcm hoot > > > I get the following error (many, many times) > mri_convert(1841) malloc: *** Deallocation of a pointer not > malloced: 0xd10ea0; This could be a double free(), or free() called > with the middle of an allocated block; Try setting environment > variable MallocHelp to see tools to help debug > > > > However, when all is said and done, I get a correct analyze file. > The binary in question is: > -rwxr-xr-x  1 frederic frederic 2034036 Feb 18 > 2004 /usr/local/freesurfer/bin/Darwin/mri_convert > > > However, if I execute: > /Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze > IM-0242-0001.dcm hoot2 > > > it returns with: > no DICOM files found. Exit > > > This binary is from the newest distribution that I have: > -rwxr-xr-x  1 frederic wheel 6236540 Jul 7 > 21:23 /Users/Shared/freesurfer/bin/mri_convert > > > So it looks like something broke. Unfortunately, I don't want to > just use the old binary, because it is missing many output formats > (particularly nii) > > > Blaise > > > > > Any information, including protected health information (PHI), > transmitted in this email is intended only for the person or entity to > which it is addressed and may contain information that is privileged, > confidential and/or exempt from disclosure under applicable Federal or > State law. Any review, retransmission, dissemination or other use of > or taking of any action in reliance upon, PHI by persons or entities > other than the intended recipient is prohibited. If you received this > email in error, please contact the sender and delete the material from > any computer. > ___ > 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
[Freesurfer] Re: Freesurfer Digest, Vol 19, Issue 49
On Sep 27, 2005, at 3:06 PM, [EMAIL PROTECTED] wrote:Message: 2Date: Tue, 27 Sep 2005 13:42:02 -0400From: Keith Schneider <[EMAIL PROTECTED]>Subject: [Freesurfer] mri_convert doesn't recognize DICOM filesTo: freesurfer@nmr.mgh.harvard.eduMessage-ID: <[EMAIL PROTECTED]>Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowedI installed Freesurfer on a G5 Tiger Mac, but mri_convert and  mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a  Siemens Trio 3T) as DICOM files. Has anyone else encountered this?Other programs can read the DICOM files just fine.keith--I have found exactly the same thing. The thing is, it _used_ to work...Using a G5 with 10.4.2, in a directory with DICOM files pulled off a Siemens Trio using Osirix, I execute the following:/usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hootI get the following error (many, many times)mri_convert(1841) malloc: *** Deallocation of a pointer not malloced: 0xd10ea0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debugHowever, when all is said and done, I get a correct analyze file. The binary in question is:-rwxr-xr-x  1 frederic frederic 2034036 Feb 18 2004 /usr/local/freesurfer/bin/Darwin/mri_convertHowever, if I execute:/Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot2it returns with:no DICOM files found. ExitThis binary is from the newest distribution that I have:-rwxr-xr-x  1 frederic wheel 6236540 Jul 7 21:23 /Users/Shared/freesurfer/bin/mri_convertSo it looks like something broke. Unfortunately, I don't want to just use the old binary, because it is missing many output formats (particularly nii)Blaise Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and/or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, PHI by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] -autorecon1/-autorecon2
Hi Michele, it may not matter. Typically we don't use the cortical aseg, but the surface-based on instead. Bruce On Tue, 27 Sep 2005, Michele Perry wrote: Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a decent portion of the meninges remain. I tried using recon-all -skullstrip -wsthresh -subjid I ran that with h=20, h=10 and h=2. It didn't seem to help so I ran recon-all ... -autorecon2 In the aseg, the meninges are labelled as cerebral cortex. There are also places where non-cerebellar areas were labelled as cerebellum cortex. Is there an automated way to fix either of these or should I fix it with manual edits? Michele ___ 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
[Freesurfer] -autorecon1/-autorecon2
Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a decent portion of the meninges remain. I tried using recon-all -skullstrip -wsthresh -subjid I ran that with h=20, h=10 and h=2. It didn't seem to help so I ran recon-all ... -autorecon2 In the aseg, the meninges are labelled as cerebral cortex. There are also places where non-cerebellar areas were labelled as cerebellum cortex. Is there an automated way to fix either of these or should I fix it with manual edits? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
Try editing those scripts so that the first line is: #!/bin/tcsh -efxv ie, adding "xv" This turns on all kinds of debugging Brian Schweinsburg, Ph.D. wrote: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 From: Doug Greve <[EMAIL PROTECTED]> Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? Can you run make_average_surface and make_average_volume separately? Brian Schweinsburg, Ph.D. wrote: I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0" Brian From: Doug Greve <[EMAIL PROTECTED]> Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 ___ 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Jeff, Can you tell me the error it is saying about MINC? Also, do you have a prior installation of the MINC tools? I am guessing you do, and that there is some prior setting of the MINC_BIN_DIR and MINC_LIB_DIR variables that is conflicting with the new installation. The MINC toolkit is included with the new distribution, so these two vars (MINC_BIN_DIR and LINC_LIB_DIR) should point into: /freesurfer/lib/mni Once that is resolved, then the freesurfer tools should be in your path. The RH9 distribution should run fine on SuSE. Nick On Tue, 2005-09-27 at 12:47 -0500, [EMAIL PROTECTED] wrote: > Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I > downloaded and installed the Redhat version, I'm not sure if this was the > correct version to use, but when I try to fix the perl path with the command > given on the wiki, it says that the command is not found, nor is nu_correct, > or > mksubjdirs, tkmedit, mri_convert, or any others that I've tried. I convert > the > shell to tcsh and source SetUpFreeSurfer.csh, and that seems to work, except > for an error about MINC. Dou you know what the issue might be with my setup? > Thanks, > Jeff > > > ___ > 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
Re: [Freesurfer] mri_convert doesn't recognize DICOM files
Keith, Can you tell me the command line use to attempt the conversion? It should be possible to convert DICOMS from a Siemens Trio 3T. Try this command-line, assuming the filename of the first slice of the structural run is called 958000-2-1.dcm: mri_convert -it dicom -ot mgz 958000-2-1.dcm 002.mgz This should produce a file called 002.mgz, which should be placed in the /mri/orig directory. If you have additional runs, be sure to name them in the same manner (###.mgz, with preceding zeroes). Nick On Tue, 2005-09-27 at 13:42 -0400, Keith Schneider wrote: > I installed Freesurfer on a G5 Tiger Mac, but mri_convert and > mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a > Siemens Trio 3T) as DICOM files. Has anyone else encountered this? > > Other programs can read the DICOM files just fine. > > keith > ___ > 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
[Freesurfer] (no subject)
Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I downloaded and installed the Redhat version, I'm not sure if this was the correct version to use, but when I try to fix the perl path with the command given on the wiki, it says that the command is not found, nor is nu_correct, or mksubjdirs, tkmedit, mri_convert, or any others that I've tried. I convert the shell to tcsh and source SetUpFreeSurfer.csh, and that seems to work, except for an error about MINC. Dou you know what the issue might be with my setup? Thanks, Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert doesn't recognize DICOM files
I installed Freesurfer on a G5 Tiger Mac, but mri_convert and mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a Siemens Trio 3T) as DICOM files. Has anyone else encountered this? Other programs can read the DICOM files just fine. keith ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
Title: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 From: Doug Greve <[EMAIL PROTECTED]> Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? Can you run make_average_surface and make_average_volume separately? Brian Schweinsburg, Ph.D. wrote: I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0" Brian From: Doug Greve <[EMAIL PROTECTED]> Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
Can you run make_average_surface and make_average_volume separately? Brian Schweinsburg, Ph.D. wrote: I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0" Brian From: Doug Greve <[EMAIL PROTECTED]> Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
