[Freesurfer] help with cortical thickness maps
Hello allI have a basic question. How do I create cortical thickness maps? I have been through most of the freesurfer tutorial and understand most of the commands. However, I am wondering how I can create a cortical thickness map for some of my own MRI data. Please let me know what steps I should take to do this. Thanks!Abi-- Abilash A. GopalDoris Duke Research Fellow, Harvard Medical SchoolMD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: help with cortical thickness maps
Hello allHello allI am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps? To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused. Please let me know if you can answer my questions.Thanks!Abi-- Abilash A. GopalDoris Duke Research Fellow, Harvard Medical SchoolMD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: help with cortical thickness maps
Hi all, below is my information.rhinal cat $FREESURFER_HOME/build-stamp.txtsource /usr/local/freesurfer/nmr-dev-envsetenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_datawhich tkmeditcd /space/rhinal/2/users/gopal/lynch_data tkmedit lynch filled.mgzerror: loading volume filled.mgzcouldn't read the anatomical volume.TKMedit couldn't read the file you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.Again, to clarify, I ran the 'recon-all' command on the lynch data, per the tutorial. However, as you can see from above, I did not create the ' filled.mgz' file, nor other files which I thought would have been created (e.g. .white, .pial, and .thickness files). How do I create these files? I thought that by running recon-all I would have created them. Please let me know what you think; I believe that this is a very basic question. ThanksAbi On 11/13/06, Doug Greve <[EMAIL PROTECTED]> wrote: Hi Abi, in general, we need more info than what you have supplied. As a new user, you are probably what is helpful info and what is not. To assist you, we have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and supply all the information is asks for. thanks! doug Abi Gopal wrote: Hello all Hello all I am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps? To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused. Please let me know if you can answer my questions. Thanks! Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School ___Freesurfer mailing listFreesurfer@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 -- Abilash A. GopalDoris Duke Research Fellow, Harvard Medical SchoolMD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: help with cortical thickness maps
I ran recon-all as follows:recon-all -i asl_12slices_180/1024.dcm -s lynchit outputted 001.mgzwhat are the steps i need to follow in order to create the 'filled.mgz' file and the other files (e.g. .white, .pial, and .thickness files)? I thought that recon-all would have taken care of the remaining steps and created these files. ThanksabiOn 11/14/06, Bruce Fischl <[EMAIL PROTECTED]> wrote: but how did you reun recon-all and what did it output?On Tue, 14 Nov 2006,Abi Gopal wrote:> Hi all, below is my information.>> rhinal>> cat $FREESURFER_HOME/build-stamp.txt >> source /usr/local/freesurfer/nmr-dev-env> setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data>> which tkmedit>> cd /space/rhinal/2/users/gopal/lynch_data>> tkmedit lynch filled.mgz>> error: loading volume filled.mgz> couldn't read the anatomical volume.>> TKMedit couldn't read the file you specified. This could be because> the image format wasn't recognized, > or it couldn't find the proper header, or the file(s) were unreadable,> or it was the wrong size.>>> Again, to clarify, I ran the 'recon-all' command on the lynch data, per the> tutorial. However, as you can see from above, I did not create the ' > filled.mgz' file, nor other files which I thought would have been created (> e.g. .white, .pial, and .thickness files). How do I create these files? I> thought that by running recon-all I would have created them. Please let me > know what you think; I believe that this is a very basic question.>> Thanks> Abi>> On 11/13/06, Doug Greve <[EMAIL PROTECTED] > wrote:>>>> Hi Abi,>>>> in general, we need more info than what you have supplied. As a new user,>> you are probably what is helpful info and what is not. To assist you, we >> have prepared the following web site:>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and>> supply all the information is asks for. >>>> thanks!>>>> doug>>>>>>>> Abi Gopal wrote:>>>> Hello all>>>> Hello all>>>> I am trying to view my outputted images from reconstruction in tksurfer. >> However, there are no files in the 'surf' folder in my subject. The 'mri'>> folder only has the orig.mgz file. How do I get the other files, such as>> .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and >> inflating' steps?>>>> To clarify, I performed the 'recon-all' command on my data set, but I only>> see the orig.mgz file. I consulted the tutorial, and using the example>> 'bert,' it showed all the outputted files in the surf folder. However, it >> does not state what actions I need to perform in order to get these files.>> In fact, it seems to suggest that the recon-all command would take care of>> all these steps. I'm a little confused. >>>> Please let me know if you can answer my questions.>>>> Thanks!>> Abi>>>> -->> Abilash A. Gopal>> Doris Duke Research Fellow, Harvard Medical School >> MD Candidate 2008, Tufts Medical School>>>> -->>>> ___>> Freesurfer mailing list>> [EMAIL PROTECTED]://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>>>>>>>-- Abilash A. GopalDoris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] visualizing ASL images
Hello all I'm new to the freesurfer mailing list, so I was hoping I could get some advice here. As part of my research, I have been acquiring arterial spin-labeling (ASL) images of subjects with cortical dysplasia (a type of brain malformation). However, I've been having problems visualizing the ASL images individually. Specifically, when I extract the ASL images in .DCM form, all 12 of them show up on a single picture. Do you know of any way to extract them individually, so that I can view a single slice on each page? I really appreciate any help you can give me. Thanks Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ASL perfusion maps
Hi all I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing. Thanks Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ASL perfusion maps
Hello all I am still having some trouble getting started on preprocessing of my ASL data. Steve Smith has suggested that I do sub-TR timing-adjustment before a subtraction analysis in FEAT. I wonder if anyone in the Martinos center has expertise with this kind of analysis. If possible, I'd like to stop by the Martinos center for a short tutorial in preprocessing ASL data. If anyone there can help me with this, please let me know. I don't think it should take too long (30 min or less), and it would really help me out, as I am quite new to all of this software. Thanks Abi On 11/27/06, Steve Smith <[EMAIL PROTECTED]> wrote: Indeed - you don't just want to do pairwise subtraction Abi, it's better to do sub-TR timing-adjustment on the tagged and control data before subtraction - if you look in the latest version of FEAT in FSL you'll see options for easy preprocessing of ASL data. You would then be able to use the normal methods for transferring FEAT data into FreeSurferSpace. Cheers, Steve. On 27 Nov 2006, at 17:47, Doug Greve wrote: > > We don't have an MC program. You can try running FSL's FLIRT or AFNI's > 3dvolreg. As for analysis, you should be able run > > mri_concat --paired-diff --mean inputaslvolume outputvolume > > I've never actually tried it like this, but it should work. > > doug > > > On Mon, 27 Nov 2006, Abi Gopal wrote: > >> Hi all >> >> I have collected some raw Arterial Spin Labeling (ASL) data. I >> would like >> to use freesurfer to create perfusion maps of this data. Is it >> possible to >> take the raw data, motion correct it, perform a pairwise >> subtraction, and >> then average all the subtractions to create a mean perfusion map? >> Please >> let me know if you have ideas on how to do this sort of thing. >> >> Thanks >> Abi >> >> > > -- > 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 --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [EMAIL PROTECTED]http://www.fmrib.ox.ac.uk/~steve --- -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
