[Freesurfer] Fake thickness map 2
-- Forwarded message -- From: Bruce Fischl <[EMAIL PROTECTED]> Date: 06/08/2007 14:23 Subject: Re: [Freesurfer] Fake thickness map 2 To: Inês Souta <[EMAIL PROTECTED]> they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros). Send these to the list so other people can answer! Bruce On Mon, 6 Aug 2007, Inês Souta wrote: > Hi again, > > I still don't understand what all the input objects of save_mgh function > stand for. 'vol' is the vector of thickness values, 'fname' is the name of > the output .mgh file, and what about M and ? What do they stand > for and how should I define them? > > Thanks again, > > Ines > > 2007/7/31, Bruce Fischl <[EMAIL PROTECTED]>: >> >> Hi Ines, >> >> use the mgh route. The "vol" is actually the vector of thickness values, >> with one entry per vertex on the surface. >> >> cheers, >> Bruce >> On Tue, 31 Jul 2007, Inês Souta >> wrote: >> >>> Hello, >>> >>> I was trying to create a cortical thickness map with constant values in >>> order to perform some tests. At first I tried using mris_convert. I >>> converted my thickness file into ascii: >>> >>> mris_convert lh.thickness lh.thickess.asc >>> >>> then I used matlab to change all the values in the last column to 2,0. I >>> tried to convert the ascii file back to surface file by doing >>> >>> mris_convert lh.thicness.asc lh.thickness >>> >>> but I got "Segmentation fault". How can I convert may ascii file into a >>> surface one? >>> >>> After failling to acomplish this, I tried using the save_mgh and >> load_mgh >>> file, nevertheless I'm not quite sure which input values are needed. >> Where >>> can I put my fake values in the save_mgh file? And what is "vol"? >>> >>> Thanks, >>> >>> Ines >>> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fake thickness map 2
freesurfer v.3.0.5 for Linux-Centos4 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > > yes, you should be able to open it in tksurfer. What version of > freesurfer do you have? > On Mon, 6 Aug 2007, Inês Souta wrote: > > > And after creating the mgh volume, how can I read it? Is it possible to > open > > it in tksurfer? Should I load it as an overlay? > > I've used one of my already pre-processed subjects, created a 'vol' with > the > > same number of vertices of one of the hemisferes, and saved the output > of > > save_mgh file as an rh.thickness.mgh file. However, when I don't seem to > be > > able to open it in tksurfer... > > > > Thanks > > > > Ines > > > > 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > >> > >> they don't matter. For a real volume they would be the ras2vox > transform > >> and the mr parameters. For your purposes they can be any 4x4 and you > can > >> leave the mri_parms one out (it will detect and fill it in with zeros). > >> > >> Send these to the list so other people can answer! > >> > >> Bruce > >> On > >> Mon, 6 Aug 2007, Inês Souta wrote: > >> > >>> Hi again, > >>> > >>> I still don't understand what all the input objects of save_mgh > function > >>> stand for. 'vol' is the vector of thickness values, 'fname' is the > name > >> of > >>> the output .mgh file, and what about M and ? What do they > >> stand > >>> for and how should I define them? > >>> > >>> Thanks again, > >>> > >>> Ines > >>> > >>> 2007/7/31, Bruce Fischl <[EMAIL PROTECTED]>: > > Hi Ines, > > use the mgh route. The "vol" is actually the vector of thickness > >> values, > with one entry per vertex on the surface. > > cheers, > Bruce > On Tue, 31 Jul 2007, Inês Souta > wrote: > > > Hello, > > > > I was trying to create a cortical thickness map with constant values > >> in > > order to perform some tests. At first I tried using mris_convert. I > > converted my thickness file into ascii: > > > > mris_convert lh.thickness lh.thickess.asc > > > > then I used matlab to change all the values in the last column to > 2,0. > >> I > > tried to convert the ascii file back to surface file by doing > > > > mris_convert lh.thicness.asc lh.thickness > > > > but I got "Segmentation fault". How can I convert may ascii file > into > >> a > > surface one? > > > > After failling to acomplish this, I tried using the save_mgh and > load_mgh > > file, nevertheless I'm not quite sure which input values are needed. > Where > > can I put my fake values in the save_mgh file? And what is "vol"? > > > > Thanks, > > > > Ines > > > >>> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fake thickness map 2
Sorry, I was saving it with the wrong extension. I am already able to open it in tksurfer! Thanks a lot, Ines 2007/8/6, Inês Souta <[EMAIL PROTECTED]>: > > freesurfer v.3.0.5 for Linux-Centos4 > > > 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > > > > yes, you should be able to open it in tksurfer. What version of > > freesurfer do you have? > > On Mon, 6 Aug 2007, Inês Souta wrote: > > > > > And after creating the mgh volume, how can I read it? Is it possible > > to open > > > it in tksurfer? Should I load it as an overlay? > > > I've used one of my already pre-processed subjects, created a 'vol' > > with the > > > same number of vertices of one of the hemisferes, and saved the output > > of > > > save_mgh file as an rh.thickness.mgh file. However, when I don't seem > > to be > > > able to open it in tksurfer... > > > > > > Thanks > > > > > > Ines > > > > > > 2007/8/6, Bruce Fischl < [EMAIL PROTECTED]>: > > >> > > >> they don't matter. For a real volume they would be the ras2vox > > transform > > >> and the mr parameters. For your purposes they can be any 4x4 and you > > can > > >> leave the mri_parms one out (it will detect and fill it in with > > zeros). > > >> > > >> Send these to the list so other people can answer! > > >> > > >> Bruce > > >> On > > >> Mon, 6 Aug 2007, Inês Souta wrote: > > >> > > >>> Hi again, > > >>> > > >>> I still don't understand what all the input objects of save_mgh > > function > > >>> stand for. 'vol' is the vector of thickness values, 'fname' is the > > name > > >> of > > >>> the output .mgh file, and what about M and ? What do they > > >> stand > > >>> for and how should I define them? > > >>> > > >>> Thanks again, > > >>> > > >>> Ines > > >>> > > >>> 2007/7/31, Bruce Fischl <[EMAIL PROTECTED]>: > > > > Hi Ines, > > > > use the mgh route. The "vol" is actually the vector of thickness > > >> values, > > with one entry per vertex on the surface. > > > > cheers, > > Bruce > > On Tue, 31 Jul 2007, Inês Souta > > wrote: > > > > > Hello, > > > > > > I was trying to create a cortical thickness map with constant > > values > > >> in > > > order to perform some tests. At first I tried using mris_convert. > > I > > > converted my thickness file into ascii: > > > > > > mris_convert lh.thickness lh.thickess.asc > > > > > > then I used matlab to change all the values in the last column to > > 2,0. > > >> I > > > tried to convert the ascii file back to surface file by doing > > > > > > mris_convert lh.thicness.asc lh.thickness > > > > > > but I got "Segmentation fault". How can I convert may ascii file > > into > > >> a > > > surface one? > > > > > > After failling to acomplish this, I tried using the save_mgh and > > load_mgh > > > file, nevertheless I'm not quite sure which input values are > > needed. > > Where > > > can I put my fake values in the save_mgh file? And what is "vol"? > > > > > > Thanks, > > > > > > Ines > > > > > >>> > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fake thickness map 2
And after creating the mgh volume, how can I read it? Is it possible to open it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with the same number of vertices of one of the hemisferes, and saved the output of save_mgh file as an rh.thickness.mgh file. However, when I don't seem to be able to open it in tksurfer... Thanks Ines 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > > they don't matter. For a real volume they would be the ras2vox transform > and the mr parameters. For your purposes they can be any 4x4 and you can > leave the mri_parms one out (it will detect and fill it in with zeros). > > Send these to the list so other people can answer! > > Bruce > On > Mon, 6 Aug 2007, Inês Souta wrote: > > > Hi again, > > > > I still don't understand what all the input objects of save_mgh function > > stand for. 'vol' is the vector of thickness values, 'fname' is the name > of > > the output .mgh file, and what about M and ? What do they > stand > > for and how should I define them? > > > > Thanks again, > > > > Ines > > > > 2007/7/31, Bruce Fischl <[EMAIL PROTECTED]>: > >> > >> Hi Ines, > >> > >> use the mgh route. The "vol" is actually the vector of thickness > values, > >> with one entry per vertex on the surface. > >> > >> cheers, > >> Bruce > >> On Tue, 31 Jul 2007, Inês Souta > >> wrote: > >> > >>> Hello, > >>> > >>> I was trying to create a cortical thickness map with constant values > in > >>> order to perform some tests. At first I tried using mris_convert. I > >>> converted my thickness file into ascii: > >>> > >>> mris_convert lh.thickness lh.thickess.asc > >>> > >>> then I used matlab to change all the values in the last column to 2,0. > I > >>> tried to convert the ascii file back to surface file by doing > >>> > >>> mris_convert lh.thicness.asc lh.thickness > >>> > >>> but I got "Segmentation fault". How can I convert may ascii file into > a > >>> surface one? > >>> > >>> After failling to acomplish this, I tried using the save_mgh and > >> load_mgh > >>> file, nevertheless I'm not quite sure which input values are needed. > >> Where > >>> can I put my fake values in the save_mgh file? And what is "vol"? > >>> > >>> Thanks, > >>> > >>> Ines > >>> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fake thickness map 2
yes, you should be able to open it in tksurfer. What version of freesurfer do you have? On Mon, 6 Aug 2007, Inês Souta wrote: And after creating the mgh volume, how can I read it? Is it possible to open it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with the same number of vertices of one of the hemisferes, and saved the output of save_mgh file as an rh.thickness.mgh file. However, when I don't seem to be able to open it in tksurfer... Thanks Ines 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros). Send these to the list so other people can answer! Bruce On Mon, 6 Aug 2007, Inês Souta wrote: Hi again, I still don't understand what all the input objects of save_mgh function stand for. 'vol' is the vector of thickness values, 'fname' is the name of the output .mgh file, and what about M and ? What do they stand for and how should I define them? Thanks again, Ines 2007/7/31, Bruce Fischl <[EMAIL PROTECTED]>: Hi Ines, use the mgh route. The "vol" is actually the vector of thickness values, with one entry per vertex on the surface. cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote: Hello, I was trying to create a cortical thickness map with constant values in order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii: mris_convert lh.thickness lh.thickess.asc then I used matlab to change all the values in the last column to 2,0. I tried to convert the ascii file back to surface file by doing mris_convert lh.thicness.asc lh.thickness but I got "Segmentation fault". How can I convert may ascii file into a surface one? After failling to acomplish this, I tried using the save_mgh and load_mgh file, nevertheless I'm not quite sure which input values are needed. Where can I put my fake values in the save_mgh file? And what is "vol"? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to do a surface-based group analysis with single-subject SPM5 contrast images
That looks exactly right. Are you experiencing a problem? I assume that uS1_v01_06LOC_x001.img is a mean functional image of some sort (and not a contrast image). Did you check the registration? doug Johannes Klackl wrote: Dear all, I'm currently trying to conduct a surface-based group analysis using 1st level contrast images from SPM5. I wanted to ask if somebody could tell me if what I'm doing is OK. I would relly appreciate your help! I will now describe the procedure: The functionals of each subject were realigned and unwarped using SPM5 preprocessing commands and then entered into an SPM 1st level designs. Additionally, of course, cortical models from all subjects were created using Freesurfer. I used spmregister to realign the contrast images (con_0001.img) with the Freesurfer anatomicals. spmregister --s v01 --mov ../f2/auS1_v01_06LOC_x001.img --reg v01_register.dat Then I used mri_vol2surf (with the resulting registration file from spmregister) to bring the volumetric information from the contrast images onto each subject's individual surface. mri_vol2surf --hemi lh --src con_0001.img --src_type analyze --srcreg v01_register.dat --out lh.con_0001.mgh --out_type mgh --projfrac 0.5 --noreshape After that, I used mri_surf2surf with ico as the target to bring all the functionals from the individual subject surface onto a common surface. mri_surf2surf --hemi lh --srcsubject v01 --srcsurfval lh.con_0001.mgh --src_type mgh --trgsubject ico --trgicoorder 7 --trgsurfval lh.ico.con_0001.mgh --trg_type mgh I was thinking about smoothing here, but I didn't do this yet. Then, I used mri_concat to concatenate the functionals from all subjects into one file and mri_glmfit to do the statistics. Thanks, Johannes Klackl, University of Salzburg ___ 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] optseq2 question about fixing null intervals
what do you mean by "allowable null intervals"? If you mean that there needs to be a fixed amount of time between two stimuli, then you cannot use optseq for this. However, you can tell optseq that there are only two stimuli, which each stimulus is a pair. Then you'd have to go back and recode the timing file. doug Denis R wrote: Hello, We're designing a task that has two pairs of events (4 events total). Each pair of events has a pair of allowable null intervals associated with it. Is it possible to use optseq2 to create such a paradigm? Is it appropriate to use optseq2 in this case at all given these constraints? ___ 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] questions
For #2, you can use mri_volsynth with --pdf checker to create a checker board pattern. You'll need a new version, which I have put here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_volsynth doug Bruce Fischl wrote: hmmm, not sure i understand. You can visualize any scalar field in the volume, so yes. As for the volume, I guess you could create a functional volume with the value in each voxel the slice # that it is in and just paint that onto the surface as normal. cheers, Bruce On Fri, 3 Aug 2007, Paul Aparicio wrote: Hello All, I have 2 questions I hope someone can help me with. 1) Is it possible to plot on a surface a set of arbitrary points in the coordinate frame of an anatomical volume? In other words if I have a set of x,y, and z points (not voxel indices: e.g. sub-voxel coordinates) can I plot them onto a surface? 2) Is there a way to view the slice lines in a volume and a surface? Can I see the anatomical location of the boundaries of the functional slices on the surface representation? Thanks paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] possible bug found in mri_surfcluster
Where is this data located? I cant find it under /space/ventzl/1/users/SUBJECTS_DIR Robert Levy wrote: Hello, I found a possible bug in mri_surfcluster, but it may be linked specifically to average7 and no other srcsubjects (but I haven't checked that). When I run mri_surfcluster with cluster simulation data, the size is reported at a seemingly arbitrary number, based on the fact that the #of vertices does not change. And the mgh output in null (a blank surface is displayed). However when I run mri_surfcluster with cluster simulation data, but specify srcsubject, it works correctly. This seems like a bug, because I think when surfcluster runs csd files it reads the srcsubject from the csd files, and no other srcsubject should be compatible with the data, therefore it must know the srcsubject in both usages, but in one case it works and the other it doesn't. Thanks, Rob surflcluster with threshold of 1.3 # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 1 -2.217 145639413.11 -6.4 38.45.0 418 2 -1.836 29811141.08-11.9 53.2 19.0 178 3 -1.532 16680111.99-11.1 19.1 22.6 178 4 -1.400 83520 17.42 -3.2 11.4 17.523 surfcluster using csd files # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHi NVtxs 1 -2.217 145639275.40 -6.4 38.45.0 0.01190 0.01050 0.01330 418 2 -1.836 29811 94.06-11.9 53.2 19.0 0.50970 0.50330 0.51610 178 3 -1.532 16680 74.66-11.1 19.1 22.6 0.64580 0.63970 0.65190 178 4 -1.400 83520 11.61 -3.2 11.4 17.5 0.97920 0.97740 0.9810023 Apparently this is the right way to do it: with csd files, but specify srcsubj average7: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHi NVtxs 1 -2.217 145639413.11 -6.4 38.45.0 0.00010 0.0 0.00020 418 2 -1.836 29811141.08-11.9 53.2 19.0 0.27000 0.26430 0.27570 178 3 -1.532 16680111.99-11.1 19.1 22.6 0.40500 0.39870 0.41130 178 4 -1.400 83520 17.42 -3.2 11.4 17.5 0.96970 0.96750 0.9719023 --- freesurfer-Linux-centos4_x86_64-dev-20070802 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl # PWD: /space/ventzl/1/users/SUBJECTS_DIR mri_surfcluster \ --src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \ --sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \ --ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \ # overlay shows no clusters (tried at 0.5 as well in case it is a binary map) tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh mri_surfcluster \ --really-use-average7 \ --src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \ --sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \ --ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \ --srcsubj average7 # overlay does show the clusters tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.ed
[Freesurfer] Banks of the superior temporal sulcus question
I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral boundaries? Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Banks of the superior temporal sulcus question
I think it's where Ron Killiany previously found large effects in prodromal AD. On Mon, 6 Aug 2007, Morgan Hough wrote: I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral boundaries? Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Banks of the superior temporal sulcus question
Hi Bruce, I see. It just seems to be surrounded by very large parcellation units that haven't been divided. Does it have good landmarks to place it along the sulcus? Cheers, -Morgan Bruce Fischl wrote: I think it's where Ron Killiany previously found large effects in prodromal AD. On Mon, 6 Aug 2007, Morgan Hough wrote: I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral boundaries? Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Banks of the superior temporal sulcus question
Hi Morgan, I'm not really sure. You could check with Ron and Rahul (ccd). cheers, Bruce On Mon, 6 Aug 2007, Morgan Hough wrote: Hi Bruce, I see. It just seems to be surrounded by very large parcellation units that haven't been divided. Does it have good landmarks to place it along the sulcus? Cheers, -Morgan Bruce Fischl wrote: I think it's where Ron Killiany previously found large effects in prodromal AD. On Mon, 6 Aug 2007, Morgan Hough wrote: I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral boundaries? Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_anatomical_stats question
I am reporting thickness values from subjects native space constrained by mask labels using mris_anatomical_stats. I am currently getting the average of the unsmoothed estimates. I would like to be able to get smoothed values but the usage reports the smoothing option as -nsmooth <#> where the # is the # of smoothing iterations. If we are using 10mm FWHM smoothing for the group results can I estimate the number of smoothing iterations to obtain something equivalent? Would it be easier to use mri_surf2surf and create a smoothed thickness file for each subject? Thanks again. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] editing labels
Hi all, I just wanted to ask about editing labels in tksurfer. I have converted my annot files to labels using mri_annotation2label, and now have all of the labels in the label directory. However when I edit the labels, and then save them using save selected label (highlighting the label and choosing the correct label in the correct hemisphere), nothing is saved when I pull up the image again. I have tried to convert the labels to annot files using mris_label2annot, but this isn't working either. I'm not sure what I am doing incorrectly. Thanks, sarah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] editing labels
Hi Sarah, When you save the label, is there any output on the shell? Can you load and edit a single label, save it out, exit tksurfer, restart it, and load the label in again, with the changes you made present in the label? On Mon, 2007-08-06 at 14:09 -0400, Sarah J Greene wrote: > Hi all, > I just wanted to ask about editing labels in tksurfer. I have > converted my annot files to labels using mri_annotation2label, and now > have all of the labels in the label directory. However when I edit > the labels, and then save them using save selected label (highlighting > the label and choosing the correct label in the correct hemisphere), > nothing is saved when I pull up the image again. I have tried to > convert the labels to annot files using mris_label2annot, but this > isn't working either. I'm not sure what I am doing incorrectly. > Thanks, > sarah -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thickness standard deviation map
The easiest thing is #2. It will produce rstd.mgh as an output, and that's what you want. Burmicz, Ryszarda wrote: Hi Freesurfers, I have tried looking this up on the list, but I don't understand exactly what to do in this scenario: I have a group of subjects (all controls). I want to create a surface map of the standard deviations of the thickness values (i.e. to show how the thicknesses vary across subjects). I am not sure what is the easiest way to go about this - can I: 1) simply convert the ?h.thickness files to .asc and calculate the deviations at each vertex (I am under the impression that this is not correct as they need to be registered to a common surface first), then convert back to .thickness and load into tksurfer 2) use mris_preproc then mris_glmfit? I don't necessarily want to calculate any stats, but I wouldn't mind a pretty picture :) If I have 4 groups of 10 subjects each, so if I churn these all through glm_fit will I be able to access separate thickness files for each group? And how can I map standard deviations for each group in this scenario? Many thanks, Rysia ___ 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] determining sizes of clusters at given CWP cutoff
I don't have an easy way to do this, sorry. Robert Levy wrote: Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance, and it appeared from the mc-corrected overlay that in this overlay the clusters do not continously change in size but appear discretely at a given threshold and are the same size at higher thresholds in an all-or-nother sort of way. I take this to mean that because the monte carlo simulation was performed at a given threshold, the clusters at that threshold size are corrected for mutiple comparisons based on the probability distribution of the chance data (though I don't know the details). Because it is done in this way, it seems I would either have to run several monte carlo simulations, at successively higher minimum thresholds, in order to arrive at the critical cutoff sizes for significance. This is impractical, so I guess my question is, does the way in which the monte carlo simulations are done preclude the possibility of getting the cluster sizes at which they will have a certain CWP value, or is there some way of doing this? Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dev version of mri_glmfit for intel macs
Hi, I'm getting a bus error when I run mri_glmfit on my Intel Mac. When I had this problem before, I got a development version of mri_glmfit which solved the problem. Unfortunately I've reinstalled a newer version of Freesurfer since then and overwrote that binary file and it's no longer on the public distribution server. If someone could repost the latest version of mri_glmfit for Intel Macs (10.4.9), that would be great. The same problem is described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html Thanks, Cate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] dev version of mri_glmfit for intel macs
Cate, There is a current dev distribution of freesurfer for the Intel Mac here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/macintel Its the .dmg file, which you can drag and drop to your desktop, then double-click to start the install GUI. A new mri_glmfit is also in that dir if you just want that. Nick On Mon, 2007-08-06 at 17:56 -0400, Catherine Hartley wrote: > Hi, > > I'm getting a bus error when I run mri_glmfit on my Intel Mac. When > I had this problem before, I got a development version of mri_glmfit > which solved the problem. Unfortunately I've reinstalled a newer > version of Freesurfer since then and overwrote that binary file and > it's no longer on the public distribution server. > > If someone could repost the latest version of mri_glmfit for Intel > Macs (10.4.9), that would be great. > > The same problem is described here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html > > Thanks, > Cate > ___ > 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
