[Freesurfer] Problem with the parcellation

Hello, I have been running freesurfer in G5 Macs with Panther. I was able to parcellate and retrieve data of the different areas. However, recently we changed the OS from Panther to Tiger. Since then, I have the following problem: When I do mris_anatomical_stats: [ogden:freesurfer_package/freesu

[Freesurfer] Gray Volume question

Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions. If I want to compare these volumes, should I normalize them with the total brain (or hemisphere) volume or can I use these results directly?

[Freesurfer] parcellated areas

Hi, when I do parcellate_subject, I received this message with one of my brains: 2816 1563 3354 2.147 +- 0.645 0.190 0.071 58.221 6.689 ** annotation 003c148c 1449858 2052 2.369 +- 0.688 0.191 0.055 26.557 2.772 ** annotation 003cdc14 1996 1206 2429

[Freesurfer] check_subject

when i put check_subject 14456, i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% check_subject 14456 CHECKING SUBJECT 14456 WARN: lh.rh.sphere.reg is empty/missing [ogden:freesurfer_package/freesurfer/subjects] wpark% is there any problem? wan

[Freesurfer] mri_convert

hi, i am trying to convert 124 slices of .dcm files COR, but when i put mri_convert E9042_S002_A0001_anon.dcm . (E9042_S002_A0001_anon.dcm is the first slice). i receive this message: %mri_convert E9042_S002_A0001_anon.dcm . mri_convert E9042_S002_A0001_anon.dcm . reading from E9042_S002_A00

Re: [Freesurfer] Problem converting IMA files

Can I suggest to change the file name from .IMA to .ima? Wan On Apr 19, 2005, at 9:14 AM, Bruce Fischl wrote: Hi Kristine, you can send us a series and we'll look at them if you want. Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: Hi Bruce I tried -it siemens too (based on some list quest

[Freesurfer] mri_convert orientation

Unfortunately I only have img/hdr files. when I put mri_info I have this message: [ash:14725/mri/orig] wpark% ls 14725.hdr 14725.img [ash:14725/mri/orig] wpark% mri_info 14725.img INFO: analyzeRead(): found 1 files for /usr/local/freesurfer_package/freesurfer subjects/14725/mri/orig/14725

[Freesurfer] parcellation II

impossible unless you've used something like vitamin E tablets in the scan. This is why we don't use analyze, unless it comes with an spm-style .mat file (which does specify the direction cosines) Bruce On Tue, 12 Apr 2005, Wan Park wrote: Hello, after parcellating some brains, I have notice

[Freesurfer] parcellation

Hello, after parcellating some brains, I have noticed that the program "get confused" and label the occipital as frontal and viceversa. I started with img/hdr images. I suspect that this occurs because of a "wrong" direction of the original image before doing mri_convert. Is it true? How can I

[Freesurfer] parcellation

Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks

[Freesurfer] Parcellation IV

Thanks Xiao Han! I worked finally! Cheers (see below) Now I have this question: I see there is a lot of regions. How do each region correspond to specific color in the visualization? Thanks a lot! Wan total white matter volume = 533145 mm^3 table columns are: number of vertices t

[Freesurfer] Parcellation III

Hi, thank you very much for your help, but now when I try to do what Quinn told me: On Mar 21, 2005, at 5:31 PM, Brian T. Quinn wrote: mris_anatomical_stats -b -a subject/label/rh.aparc.annot subject rh I receive the following error (15058 is the subject): [ogden:freesurfer_package/freesurfer

[Freesurfer] Parcellation II

cheers! i did exactly the same thing with another brain but this time i obtained this which looks much better: <> (i am sending this again in a smaller size to avoid the mediator) i guess this is correct. now, how can i use this areas to calculate the gray matter volume of these "standard areas"

[Freesurfer] Parcellation

Hello, I need to parcellate the brain in "standard areas" (eg. prefrontal, occipital, temporal, etc.). I have a MAC and I did the parcellation with the new binaries that Kevin Teich sent me. What I have is a multicolor brain painted in tiny pieces. Is this correct? What I am interested is to c

[Freesurfer] new tkmedit and tksurfer

I am supposed to have libtiff, glut, tclkt, tix and blt installed, but I still receive this message: for volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /

Re: [Freesurfer] new binaries for tkmedit and tksurfer

PM, Kevin Teich wrote: Do you have BLT installed via Fink or FinkCommander? On Sun, 13 Feb 2005, Wan Park wrote: hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bi

[Freesurfer] new binaries for tkmedit and tksurfer

hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i

[Freesurfer] MNI align

I think I need to do the MNI align. Could someone teach me how to do this? Thanks, Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] about tkmedit

after processing the volume, when i try to see the images (orig, T1, brain, wm) with the tkmedit tools, i press coronal view but i see horizontal and when i press horizontal i see the coronal view. when i press sagittal, i see the brain "looking" (face) down. interestingly, after doing the tala

[Freesurfer] error in the visualization of the parcellation

hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 1

[Freesurfer] visualizing the parcellation 2

This is the output for the parcellate_subject: [autologins-Computer:stem/freesurfer/subjects] wanpark% parcellate_subject cf1 reading atlas from /Users/wanpark/Desktop/FreeSurfer/freesurfer/average/lh.atlas2002_simple.gcs reading color table from GCSA file input 1: CURVATURE FILE, flags 0, av

[Freesurfer] visualizing the parcellation

Hi, while I am solving the problems with the cutting planes, I am doing parcellation with the subjects that went through. After doing parcellate_subject cf1 I wanted to visualize it so I wrote tksurfer cf1 rh inflated and then I went to file>labels>annotation and wrote /Users/../Volumes/stem/fr

[Freesurfer] Re: How to fix Perl module path

l bin location use lib "$FindBin::Bin/../lib/perl5/site_perl/5.8.0"; You have to modify ../lib/perl5/site_perl/5.8.0 to suite your installation. We will be fixing this problem in the coming release, using the relative path for the module. I don't know when at this time. Tosa Wa

[Freesurfer] how to seed points 3

Hi, To create the surface, I have to define the corpus callosum and the pons as well. I have been suggested to get a talairach transform first, so I did: (22970 is the subject folder) $ talairach 22970 but I have received this message: wpark% talairach 22970 registering 22970 mri_convert orig o

[Freesurfer] how to seed points 2

Hello, Because I had problems finding automatically the corpus callosum cutting plane, I loaded the wm volume, click in the center of the corpus in coronal view, switch to sagittal plane and used the volume RAS coordinates (tailarach coord says "none"). then I ran this line: recon-all -stage2 -c

[Freesurfer] how to seed points

when i try to create the surface, i receive this message: /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ponscall.dat /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/wm /u

[Freesurfer] how to visualize the parcellation

hi, after doing: recon-all -stage4b -subjid 40032 -hemi lh recon-all -stage4b -subjid 40032 -hemi rh, i did: parcellate_subject 40032 and it seems to have finished without problems. now, how can i visualize the different areas? thanks, wan ___ Freesurfe

[Freesurfer] Parcellation 2

Thanks for the previous help! Now I have this problem: setenv CSURF_DIR $FREESURFER_HOME [ash:local/freesurfer_package/freesurfer] wpark% cd subjects [ash:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 40032 reading atlas from /usr/local/freesurfer_package/freesurfer/average

[Freesurfer] parcellation

Hi, I am want to parcellate my brains, but when I put "parcellate_subject" alone, I receive the following message; tcsh: CSURF_DIR: Undefined variable What should I do? Second question: Let's say my subject is called bert What's the complete line I should right to do it? Thanks a lot, Wan ___

[Freesurfer] question

I want to calculate the gray matter volume in certain areas (eg. cortical area 39). What should I do? Thanks, Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] filling the white matter

when I run recon-all -s uf1 -talairach (uf1 is the subject) I receive this message: $ ### INFO: SUBJECTS_DIR is /Volumes/stem/freesurfer/subjects - Talairach Fri Oct 29 17:23:19 ADT 2004 /Volumes/stem/freesurf

[Freesurfer] MNI auto talairaching

could you please tell me how to do auto talairaching with the MINC? thanks wan ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] when I am creating the surface

I start with the filling of white matter but after a while I am receiving this massage: (...) using +/- offset search region where offset is 45. using +/- offset search region where offset is 48. /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such

[Freesurfer] could you please tell me how to use mris_anatomical_stats?

or where I can read more about it? Thanks, Wan ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Hi, question

After processing the volume, creating the surface, making the final surface and registering the surface, I would like to measure the cortical thickness with freesurfer. Could you please give me hints about how and where to start? thanks Wan Park

[Freesurfer] Stripping the skull

I am having problems stripping the skull. I am converting DIACOM files into COR. Do you think that it is a problem of convertion? Should I use any extension for mri_convert? I checked the original files and the image seems to be quite Ok (I used MRIConvert and then opened with medx). I will tha

[Freesurfer] Question

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a

[Freesurfer] question

Hello, I used mri_convert to transform DIACOM files to COR files. I want now to do the structural scan but I guess I need to obtain I files (eg. I.001). How can I do that? Thanks, Wan Park ___ Freesurfer mailing list [EMAIL PROTECTED] https