Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/ FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version. It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded? Thanks, Koen On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: Hi Ed, Can you please do grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt and let me know what the result is? Thanks, and sorry this seems so difficult to sort out. Koen On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011. Ed On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version. It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded? Thanks, Koen On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: Hi Ed, Can you please do grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt and let me know what the result is? Thanks, and sorry this seems so difficult to sort out. Koen On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/ FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled (bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled (bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mapping pf fsaverage surface to native volume
Dear Freesurfer users, I've been trying to map a Qdec contrast sig.mgh to the native volume of a subject using mri_surf2surf (to get from Qdec fsaverage surface to native surface) and mri_surf2vol (to map from native surface to native volume cortical ribbon). However, the last step goes wrong: I get a nii with the same range of values as were in the surface, but the nonzero voxels are scattered all over, so I guess there is something wrong with the surface-to-voxel coordinate mapping. Below is my code, any ideas on what goes wrong? Best regards, Rene mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freesurfer base file question
Doug or any freesurfer experts can you please answer this question it is quite urgent: I have created some manual cortical labels in freesurfer using tksurfer. The .labels file containing the vertices of the cortical labels does not correspond to the labels of the pial surface even though they were drawn on the pial. I noticed however, that they do correspond to the lh.base.mgh and rh.base.mgh file that was created with an older version of freesurfer. These files contain coordinates and their corresponding label in the look up table. My guess is that the base file is an intermediate surface between the white and gray. The question is why do the vertices in the manual labels not correspond to the those in the pial surface? Alternatively, since the lh.base.mgh and rh.base.mgh are no longer apart of the recon-all process is there another name in to which it is called? The command to make the cortical label is: mri_label2vol--label labelname.label --temp brainmask.mgz --o labelname.nii.gz --identity --proj frac 0 1 .1 --subject subject_id --hemi lh The command(s) to make the base file an ascii file is: mri_annotation2label --subject # --hemi *h --seg #/surf/*h.base.mgh --outdir junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc Thank you, Tina Jeon -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 12:50 PM To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer base file question Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug On 04/02/2012 11:55 AM, Tina Jeon wrote: Hi Doug could you please answer these questions that I posted on the listserv. Your help would be much appreciated to an upcoming project on cortical development. Thank you. I noticed that the newest version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? i.e. called a different name? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon -- -- UT Southwestern Medical Center The future of medicine, today. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_label2vol cannot allocate memory
Hello Bruce, Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested. Anthony [miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a =15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s =-6.8289 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0. 0. 0. 1. voxel-to-ras determinant 0.645035 ras to voxel transform: 1.2367 0.0293 -0.009964.4661 -0.0235 1.0243 0.099536.5272 0.0125 -0.1175 1.211753.5256 0. 0. 0. 1. [miles:[PATH]] adick% mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 6.0377 : x_a = 0., y_a = 0., z_a = 1., c_a =60.9280 : x_s = 0., y_s = -1., z_s = 0., c_s =-1. talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 134.0377 0. 0. 1. -67.0720 0. -1. 0. 127. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 134.0377 -0. -0. -1. 127. -0. 1. -0.67.0720 0. 0. 0. 1. [miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory On 3/7/12 9:17 AM, Bruce Fischl wrote: Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony 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. -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi Ed, It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt. To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands: cd $FREESURFER_HOME sed -i s/CA2_3/CA2\/3/g FreeSurferColorLUT.txt sed -i s/CA4_DG/CA4\/DG/g FreeSurferColorLUT.txt Thanks, Koen On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011. Ed On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version. It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded? Thanks, Koen On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: Hi Ed, Can you please do grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt and let me know what the result is? Thanks, and sorry this seems so difficult to sort out. Koen On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_label2vol enquiry
Hi Can anyone tell me please how mri_label2vol works, I know what it does, but I need to know how it works to take the FS space to the original anatomy space: does it do registration or does it use a transformation matrix. If the latest which one, where can I find it? regards -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgad...@uic.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] Qdec issue
Hi Nick, Here's the error that I'm getting: asegstats2table --meas volume --tablefile /mnt/haley/Sonya/qdec/stats_tables/aseg.volume.stats.dat --subjects 1001 1002 1003 1004 1005 1006 1009 1010 1012 1013 1014 1015 1016 1017 1018 1020 1022 1023 1024 1025 1028 1029 1030 1031 1033 1034 1036 1037 1038 1039 1042 1045 1048 1050 1052 1054 1055 1056 1057 1058 1059 1061 1063 1066 1067 1070 1071 1072 1073 1074 1076 1079 1080 1082 1089 1098 1099 1100 1102 1103 1104 1106 1107 1108 1113 1115 1120 1121 1123 1124 1125 1127 1128 1129 1132 1133 1135 1136 1137 1138 1140 1144 1146 1147 1148 1151 Building the table.. SUBJECTS_DIR : /mnt/haley/Sonya ERROR: cannot find /mnt/haley/Sonya/1005/stats/aseg.stats Use --skip flag if you want to continue in such cases [nsilab-07:/mnt/haley/Sonya] sk27829% ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x6918ef0): Script: vtkTemp3 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --meas volume --tablefile /mnt/haley/Sonya/qdec/stats_tables/aseg.volume.stats.dat --subjects 1001 1002 1003 1004 1005 1006 1009 1010 1012 1013 1014 1015 1016 1017 1018 1020 1022 1023 1024 1025 1028 1029 1030 1031 1033 1034 1036 1037 1038 1039 1042 1045 1048 1050 1052 1054 1055 1056 1057 1058 1059 1061 1063 1066 1067 1070 1071 1072 1073 1074 1076 1079 1080 1082 1089 1098 1099 1100 1102 1103 1104 1106 1107 1108 1113 1115 1120 1121 1123 1124 1125 1127 1128 1129 1132 1133 1135 1136 1137 1138 1140 1144 1146 1147 1148 1151 Sonya On Tue, Mar 27, 2012 at 11:26 PM, sonya kaur sonya.kau...@gmail.com wrote: Hi everyone, I realize I'm quickly becoming an annoyance, but I'm having trouble loading my data file into qdec. I keep getting the error: QdecDataTable::Load failed to tokenize string: on line 88 of HTN_FMRI_Qdec. HTN_FMRI_Qdec is the name of my data file. I do not even have a line 88 as I have only 86 subjects and 4 variables. Thank you! Sonya -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E sonya_k...@mail.utexas.edu sonya_k...@mail.utexas.edu -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E sonya_k...@mail.utexas.edu sonya_k...@mail.utexas.edu ___ Freesurfer mailing list 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] hippocampal segmentation
Hello, I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image as underlay. For some subjects the hippocampus is not at the correct position. Please advise. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ Freesurfer mailing list 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.
Re: [Freesurfer] hippocampal segmentation
Hi Rashmi does it look correct in our visualization tools? If so, you'll need to talk to the AFNI folks. cheers Bruce On Wed, 4 Apr 2012, Rashmi Singh wrote: Hello, I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image as underlay. For some subjects the hippocampus is not at the correct position. Please advise. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ Freesurfer mailing list 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] Questions about recon-all process flow in build 5.0.0
Hi, I have a few questions about the process flow for the last stable build (5.0.0). After looking over http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all , https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable , and http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags , it looks like there's some inconsistency in the info on these pages that's left me a bit confused about what processing steps are and aren't invoked by autorecon2-wm, and autorecon-pial. On the 'Other Useful Flags' page, it looks as though autorecon2-wm doesn't invoke maskbfs / mri_mask, but on the recon-all page as well as in the mailing list archives it's said that autorecon2-wm runs processes both prior to autorecon2-pial and including the processes called on by autorecon2-pial. (By the way, is autorecon-pial a separate command from autorecon2-pial? Is the only difference that the former runs all the autorecon3 steps whereas the latter ends at the last step of autorecon2?) If autorecon2-wm doesn't run maskbfs / mri_mask, then wouldn't a subject who has both had pial edits done to their brainmask.mgz and wm edits done to their wm.mgz end up generating parcellation stats that don't reflect the pial edits? If that's the case, then would adding a -maskbfs flag before autorecon2-wm and -autorecon3 solve the problem? And autorecon2-cp starts with -normalization2, right? On the http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page it says that it starts running at -normalization, which would be far earlier in the pipeline. Finally, should one always wait to make pial edits or WM edits after adding control points and reprocessing from autorecon2-cp? It looks to me as though throwing control points and WM edits and/or pial edits simultaneously at a reprocessing stream wouldn't pose any problems for the file dependencies, but that you might be able to do better pial and/or WM edits after seeing the newly generated surfaces and the newly segmented wm.mgz after recon-all has incorporated the control points. Thanks so much for your help! Warren -- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freesurfer base file question
Hi Tina, sorry for the delay. Most of us are involved in the FS finishing up today. We don't know anything about a base file created by recon-all. It looks like your created it with mri_annotation2label? If so, then it is not a surface, and I'm not sure what mris_convert would do with it. I'm confused as to what you are trying to do. Can you give more detail? doug On 04/04/2012 10:52 AM, Tina Jeon wrote: Doug or any freesurfer experts can you please answer this question it is quite urgent: I have created some manual cortical labels in freesurfer using tksurfer. The .labels file containing the vertices of the cortical labels does not correspond to the labels of the pial surface even though they were drawn on the pial. I noticed however, that they do correspond to the lh.base.mgh and rh.base.mgh file that was created with an older version of freesurfer. These files contain coordinates and their corresponding label in the look up table. My guess is that the base file is an intermediate surface between the white and gray. The question is why do the vertices in the manual labels not correspond to the those in the pial surface? Alternatively, since the lh.base.mgh and rh.base.mgh are no longer apart of the recon-all process is there another name in to which it is called? The command to make the cortical label is: mri_label2vol--label labelname.label --temp brainmask.mgz --o labelname.nii.gz --identity --proj frac 0 1 .1 --subject subject_id --hemi lh The command(s) to make the base file an ascii file is: mri_annotation2label --subject # --hemi *h --seg #/surf/*h.base.mgh --outdir junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc Thank you, Tina Jeon -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 12:50 PM To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer base file question Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug On 04/02/2012 11:55 AM, Tina Jeon wrote: Hi Doug could you please answer these questions that I posted on the listserv. Your help would be much appreciated to an upcoming project on cortical development. Thank you. I noticed that the newest version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? i.e. called a different name? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon -- -- UT Southwestern Medical Center The future of medicine, today. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_label2vol enquiry
If you pass it a registration (--reg) then it uses that. It can also compute a registration from the information about the geometry in the header (--regheader) (assuming that the two volumes share a coordinate system). doug On 04/04/2012 01:48 PM, Johnson wrote: Hi Can anyone tell me please how mri_label2vol works, I know what it does, but I need to know how it works to take the FS space to the original anatomy space: does it do registration or does it use a transformation matrix. If the latest which one, where can I find it? regards -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Mapping pf fsaverage surface to native volume
How are you visualizing the results? Can you send a pic? You should be using tkmedit. doug On 04/04/2012 09:59 AM, René Besseling wrote: Dear Freesurfer users, I've been trying to map a Qdec contrast sig.mgh to the native volume of a subject using mri_surf2surf (to get from Qdec fsaverage surface to native surface) and mri_surf2vol (to map from native surface to native volume cortical ribbon). However, the last step goes wrong: I get a nii with the same range of values as were in the surface, but the nonzero voxels are scattered all over, so I guess there is something wrong with the surface-to-voxel coordinate mapping. Below is my code, any ideas on what goes wrong? Best regards, Rene mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii ___ 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 gr...@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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2vol cannot allocate memory
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh doug On 04/04/2012 12:29 PM, Anthony Dick wrote: Hello Bruce, Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested. Anthony [miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a =15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s =-6.8289 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0. 0. 0. 1. voxel-to-ras determinant 0.645035 ras to voxel transform: 1.2367 0.0293 -0.009964.4661 -0.0235 1.0243 0.099536.5272 0.0125 -0.1175 1.211753.5256 0. 0. 0. 1. [miles:[PATH]] adick% mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 6.0377 : x_a = 0., y_a = 0., z_a = 1., c_a =60.9280 : x_s = 0., y_s = -1., z_s = 0., c_s =-1. talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 134.0377 0. 0. 1. -67.0720 0. -1. 0. 127. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 134.0377 -0. -0. -1. 127. -0. 1. -0.67.0720 0. 0. 0. 1. [miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory On 3/7/12 9:17 AM, Bruce Fischl wrote: Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony 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 gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_label2vol enquiry
so how it is used here? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz On 04/04/2012 3:38 PM, Douglas N Greve wrote: If you pass it a registration (--reg) then it uses that. It can also compute a registration from the information about the geometry in the header (--regheader) (assuming that the two volumes share a coordinate system). doug On 04/04/2012 01:48 PM, Johnson wrote: Hi Can anyone tell me please how mri_label2vol works, I know what it does, but I need to know how it works to take the FS space to the original anatomy space: does it do registration or does it use a transformation matrix. If the latest which one, where can I find it? regards -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgad...@uic.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2vol cannot allocate memory
No, but the conversion from the original .nii works... [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory [miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz... On 4/4/12 4:47 PM, Douglas N Greve wrote: Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh doug On 04/04/2012 12:29 PM, Anthony Dick wrote: Hello Bruce, Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested. Anthony [miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a =15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s =-6.8289 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0. 0. 0. 1. voxel-to-ras determinant 0.645035 ras to voxel transform: 1.2367 0.0293 -0.009964.4661 -0.0235 1.0243 0.099536.5272 0.0125 -0.1175 1.211753.5256 0. 0. 0. 1. [miles:[PATH]] adick% mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 6.0377 : x_a = 0., y_a = 0., z_a = 1., c_a =60.9280 : x_s = 0., y_s = -1., z_s = 0., c_s =-1. talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 134.0377 0. 0. 1. -67.0720 0. -1. 0. 127. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 134.0377 -0. -0. -1. 127. -0. 1. -0.67.0720 0. 0. 0. 1. [miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory On 3/7/12 9:17 AM, Bruce Fischl wrote: Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running
Re: [Freesurfer] mri_label2vol cannot allocate memory
What version are you using? One of our versions had a problem with creating bad mgzs. You probably don't need to convert it to mgz. Can you run mri_label2vol with the original nii and see if it works? doug On 04/04/2012 04:50 PM, Anthony Dick wrote: No, but the conversion from the original .nii works... [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory [miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz... On 4/4/12 4:47 PM, Douglas N Greve wrote: Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh doug On 04/04/2012 12:29 PM, Anthony Dick wrote: Hello Bruce, Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested. Anthony [miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a =15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s =-6.8289 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0. 0. 0. 1. voxel-to-ras determinant 0.645035 ras to voxel transform: 1.2367 0.0293 -0.009964.4661 -0.0235 1.0243 0.099536.5272 0.0125 -0.1175 1.211753.5256 0. 0. 0. 1. [miles:[PATH]] adick% mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 6.0377 : x_a = 0., y_a = 0., z_a = 1., c_a =60.9280 : x_s = 0., y_s = -1., z_s = 0., c_s =-1. talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 134.0377 0. 0. 1. -67.0720 0. -1. 0. 127. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 134.0377 -0. -0. -1. 127. -0. 1. -0.67.0720 0. 0. 0. 1. [miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheaderchuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory On 3/7/12 9:17 AM, Bruce Fischl wrote: Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On
[Freesurfer] Stylus Input for Cortical Edits
Hi All, We have a large number of subjects that need minor edits (orbital frontal cortex/eye issues subcortical parcellation etc.). To speed up the process I was wondering if a stylus input would help with the editing. Do the graphics tablets (stylus input) work with freesurfer editing? Do they end up being useful or is it not worth investing in? And if so, could someone recommend a brand (wacom?) that would work with Ubuntu 10.04 (or just linux in general). Thank you, Jeff Stout___ Freesurfer mailing list 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.
Re: [Freesurfer] Stylus Input for Cortical Edits
We have found Wacom tablets are excellent for editing. On Apr 4, 2012 4:40 PM, Jeff Stout jstout...@yahoo.com wrote: Hi All, We have a large number of subjects that need minor edits (orbital frontal cortex/eye issues subcortical parcellation etc.). To speed up the process I was wondering if a stylus input would help with the editing. Do the graphics tablets (stylus input) work with freesurfer editing? Do they end up being useful or is it not worth investing in? And if so, could someone recommend a brand (wacom?) that would work with Ubuntu 10.04 (or just linux in general). Thank you, Jeff Stout ___ Freesurfer mailing list 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 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.
Re: [Freesurfer] lobar WM volumes
Hi Doug- I wanted to follow up on this procedure and ask for a bit of clarification. As an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' lobar volume with both WM and GM for both RH and LH. 1: mri_annotation2label --s subject --hemi rh --lobesStrict lobe mri_annotation2label --s subject --hemi lh --lobesStrict lobe 2(a): mri_aparc2aseg --s subject --labelwm --annot lobe 2(b) mri_aparc2aseg --s subject --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe I'm not sure if this the correct syntax to be analogous to that for WM in 2(a). What would be the correct syntax to combine 2(a) and 2(b) into one command? 3: Per your suggestion for syntax, this can be found in recon-all.log following that for wmparc (and I have identified that). There is similar syntax for GM/ctx. I'm not sure if the following would need to be slightly modified for my objective: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject subject But, before proceeding with the step 3, how can one determine the lobar label numbers assigned such that a custom LUT can be created. The output of the 2(b) (if the syntax is correct) indicates that 8 entries are read (Frontal, Temporal, Parietal, Occipital for LH and RH?). Thanks for your help. -Wil |-Original Message- |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] |Sent: Monday, April 02, 2012 10:39 AM |To: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] lobar WM volumes | |use mri_segstats. You can look in subjid/scripts/recon-all.log for example |command lines (look for the one with wmparc). The command will require a |color table. The ones in the log file will use the default table, but this will not |have the numbers/names of your lobar regions, so you'll need to create a |new color table (or add to the one that is there). |doug | |On 04/02/2012 12:58 PM, Inês Violante wrote: | Dear all, | | I need to obtain the white matter volume per lobe for a given numer of |subjects. | I started by using the following: | | mri_annotation2label --subjectsubjid --hemi rh --lobesStrict lobe | | mri_aparc2aseg --ssubjid --labelwm --annot lobe | | and now I have a lobe+aseg.mgz file. How can I create a stats file | containing the wm volume for each lobe? | | Thank you, | | ines | | ___ | 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 |gr...@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 | ___ Freesurfer mailing list 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] white matter hyper intensities
a collaborator just got a grant review that claimed There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesurfers ability to detect the white matter/grey matter boundary rather than cause an error. any comments as to the correctness of my thinking would be appreciated. thank you greg ___ Freesurfer mailing list 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.
Re: [Freesurfer] white matter hyper intensities
Hi Greg, I would say there are a variety of possible confounds for cortical thickness (e.g. changes in cortical myelin content, changes in the closeness of opposition between grey matter and the dura from brain atrophy), but that wouldn't be one of the ones I would think of. White matter hyperintensities tend to be most visible in T2w images (especially FLAIR), and not so much in T1w images (in fact, they might actually make T1w images darker). They also tend to be in deep white matter away from the cortex. The insula tends to be a hard place to reconstruct surfaces because the white matter is thin and not very bright (and has the grey matter claustrum interposed between the external and extreme capsules). A difference in the white matter or claustrum could well create a problem reconstructing the surface there, but I wouldn't expect a white matter hyperintensity there. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Gregory Kirk Sent: Wednesday, April 04, 2012 11:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] white matter hyper intensities a collaborator just got a grant review that claimed There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesurfers ability to detect the white matter/grey matter boundary rather than cause an error. any comments as to the correctness of my thinking would be appreciated. thank you greg ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
