[Freesurfer] recon-all exited with errors
Hello all, I was running recon-all for one of my images and this happened to be the error that i got.Could someone please clarify, Thanks in advance Chacko. mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] About FreeSurfer
Hi Ruma, we don't support IRIX anymore. And no, tiff is not one of the supported input formats, although you can save images of results to tiff. Is that what you meant? Not sure what you mean by raster based imaging. We take MRI volumes as input. cheers, Bruce On Thu, 27 Jul 2006, M SAMANTA wrote: Hello, I am interested in using FreeSurfer for my task. I have read the site about getting started. I would like to know if FreeSurfer is supported by SGI IRIX and if it is raster based imaging or understands it? I need to know specifically if TIFF images can be supported by FreeSurfer. Thanks, Ruma ___ 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] Edit label
Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Edit label
Hi Dhruman, Sorry, I meant 'occipital' not 'temporal' lobe. rahul On Thu, 27 Jul 2006, Rahul Desikan wrote: Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Edit label
Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] caudate/putamen values for mri_segstats
Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Edit label
I think that mri_mergelabels will do all the steps that Rahul describes below for you. You can input as many labels as you want (i think) and specify an output name. USAGE: mri_mergelabels -i label1 -i label2 ... -o outputlabel good luck, Jenni On Thu, 27 Jul 2006, Rahul Desikan wrote: Hi Dhruman, To the best of my knowldge, the wiki page does not contain any information on using tksurfer to add labels together. My suggestion would be the following: 1) Load the subject in using tksurfer (tksurfer subjectname hemi inflated) 2) Load in the parcellation you want to edit (e.g. rh.aparc.annot) 3) Click on a label of interest to you (e.g. caudalmiddlefrontal) 4) Then, click the 'Custom Fill' button in the Tksurfer Tools window. This button looks like a paint can and can be found in the second row of the Tksurfer Tools window. Keep this 'Custom Fill' window open for later (see steps 5-8 below). 5) Choose only the 'Up to other labels' option in the 'Custom Fill' options bar 6) In the tksurfer window where you can see the rh.aparc.annot file loaded and the inflated surface, click on a label you would like to add (e.g. rostralmiddlefrontal). 7) Then go to the 'Action' portion of the 'Custom Fill' options bar and choose 'Add to existing label'. If you look at the label bar below, it should show you which label you are adding to. 8) Repeat steps 6 and 7 for all labels you would like to add to the original one you have already selected (e.g. add rostralmiddlefrontal, superiorfrontal, precentral, parsopercularis, etc.--to caudalmiddlefrontal, the label you had already selected). 9) Once you have selected all the labels you would like to have added together, click the new label, make sure it is highlighted and save it as a new label (e.g. rh.frontal.label) I am including an image that shows what the final result might look like for the frontal lobe (lateral view) once you have added together all of your frontal subregions together. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Edit label
Almost. You'll need to run mri_annotation2label to extract the individual labels from the annot, then use mri_mergelabels to merge the ones you want. doug Jenni Pacheco wrote: I think that mri_mergelabels will do all the steps that Rahul describes below for you. You can input as many labels as you want (i think) and specify an output name. USAGE: mri_mergelabels -i label1 -i label2 ... -o outputlabel good luck, Jenni On Thu, 27 Jul 2006, Rahul Desikan wrote: Hi Dhruman, To the best of my knowldge, the wiki page does not contain any information on using tksurfer to add labels together. My suggestion would be the following: 1) Load the subject in using tksurfer (tksurfer subjectname hemi inflated) 2) Load in the parcellation you want to edit (e.g. rh.aparc.annot) 3) Click on a label of interest to you (e.g. caudalmiddlefrontal) 4) Then, click the 'Custom Fill' button in the Tksurfer Tools window. This button looks like a paint can and can be found in the second row of the Tksurfer Tools window. Keep this 'Custom Fill' window open for later (see steps 5-8 below). 5) Choose only the 'Up to other labels' option in the 'Custom Fill' options bar 6) In the tksurfer window where you can see the rh.aparc.annot file loaded and the inflated surface, click on a label you would like to add (e.g. rostralmiddlefrontal). 7) Then go to the 'Action' portion of the 'Custom Fill' options bar and choose 'Add to existing label'. If you look at the label bar below, it should show you which label you are adding to. 8) Repeat steps 6 and 7 for all labels you would like to add to the original one you have already selected (e.g. add rostralmiddlefrontal, superiorfrontal, precentral, parsopercularis, etc.--to caudalmiddlefrontal, the label you had already selected). 9) Once you have selected all the labels you would like to have added together, click the new label, make sure it is highlighted and save it as a new label (e.g. rh.frontal.label) I am including an image that shows what the final result might look like for the frontal lobe (lateral view) once you have added together all of your frontal subregions together. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman ___ 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] caudate/putamen values for mri_segstats
Hi Thang, putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look? Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote: Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
