[Freesurfer] brain stem elimination

Hi all, I ran 'process volume' and 'create surface' and found that brain stem was attached to the left inflated brain. So, I editted 'wm' slices and got rid of the parts related to the brain stem in all slices. and ran 'create surface' again, but no change took place in the 'inflated brain'!!! Wo

[Freesurfer] error in 'create surface'

Hi all, I posted a question, but for some reason, I didn't get any response. Please help me on this. Here is the question. I ran 'process volume' and 'create surface' on csurf. The created surface (left inflated) has brain stem attached to it. So, I editted 'wm' slices to get rid of it, and ran '

Re: Re: [Freesurfer] error in 'create surface'

be a bad Talairach alignment. The tutorial discusses this. Note: you should not see the brain stem after the image has been skull-stripped (which occurs during the -autorecon1 stage). Nick On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote: > Hi all, > > I posted a question, but for

[Freesurfer] errors in library in new version of Freesurfer

I installed the new version of Freesurfer by downloading from Freesurfer Wiki website. Then, I ran recon-all -subjid subjectname -autorecon1, and got the following library errors. Would someone suggest a solution? Nam. mri_convert: error while loading shared libraries: libgsl.so.0: cannot open s

Re: [Freesurfer] errors in library in new version of Freesurfer

fer. Nam. >>> Nick Schmansky <[EMAIL PROTECTED]> 06/06/06 4:42 PM >>> What is the output when this is typed: source $FREESURFER_HOME/SetUpFreeSurfer.csh and this: ldd `which mri_convert` and what OS is this installed on? On Tue, 2006-06-06 at 15:24 -0400, Joongnam Yang

[Freesurfer] inflated surface not seen

Hi all, I've run recon-all -autorecon1 and -autorecon2, successfully. But when I opened inflated surface using tksurfer, only a tiny bit of image of the inflated surface was seen. Something was wrong in the process. Both wm, filled, brain volumes looked OK. Here is the data on the web; http://www

[Freesurfer] Finding ROI and average

Hi All, Is there a method of isolating an area of the overlay image (functional onto anatomical) on Freesurfer as ROI and get the average of the amplitude of the ROI? Any suggestions would be appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr

Re: Re: [Freesurfer] Finding ROI and average

ically or functionall? You can do both. Anatomically you can use any of the cortical parcellation or subcortical segmentation units for this, or draw one yourself. On Mon, 19 Jun 2006, Joongnam Yang wrote: > Hi All, > > Is there a method of isolating an area of the overlay image (func

Re: [Freesurfer] mris_flatten missing 4 lib

Dear all, I did occipital cortex flattening and when I tried to display it on tksurfer using "tksurfer average lh occip.patch.flat", I got the following error message, which I have never seen. (the error message on memory) surfer: current subjects dir: /home/nam/AVERAGE surfer: not in "scripts"

[Freesurfer] flattened but two surfaces

Hi all, I flattened the occipital cortex and viewed it with tksurfer, but there are two flattened surfaces, top and bottom on the tksurfer window. Usually from my experience, there is one flattened surface. Could someone suggest what might have gone wrong? Nam. __

[Freesurfer] mri_vol2surf error

Dear all, I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w -

[Freesurfer] why no answer?

I posted the following question again, since I didn't get any response. I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh

[Freesurfer] posting a question again

Dear all, I've been waiting for an answer to the following question. I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --

Re: [Freesurfer] posting a question again

One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf Run it with --tfmt curv doug

[Freesurfer] mri_vol2surf warnings

Hi all, When I ran mri_vol2surf to turn FSL output to a paint file that Freesurfer can read, I got the following error. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented But the command ran through and paint files were produced. My que

[Freesurfer] strange overlay of averages

Hi all, I have a functional average (using FSL group analysis) and an anatomical average (using Freesurfer make_average_subject) across 6 subjects. (The functional average shows strong activation patterns in FSL ouput, report.html) However, when I overlay the averages, the expected functional ac

[Freesurfer] lh.thickness error

Hi all, I was doing mri_vol2surf to overlay functional average(FSL) onto anatomical average (Freesurfer) and got the following error message, ERROR: .. Reading thickness /home/nam/V4RET/average/surf/lh.thickness MRISreadCurvature: could not open /home/nam/V4RET/average/surf/lh.thi

[Freesurfer] tksurfer window too small

Hi all, When I displayed a flattened image of the entire cortex (lh.full.patch.flat) on the tksurfer window, the image was too big for the tksurfer window, meaning the falttened image is chopped out. Is there any way that I can display the entire flattened image on the tksurfer window? Thanks.

[Freesurfer] (no subject)

Hi, I used the following command recon-all -stage1 -subjid blobby and I got the following error message (Please let me know what is wrong with Freesurfer). -- copy of the exact error messages --- program versions used $Id: rec

Re: [Freesurfer] (no subject)

nvironment variables for the MNI package? Nam. >>> Bruce Fischl <[EMAIL PROTECTED]> 10/19/04 3:16 PM >>> it looks like you don't have the MNI software installed (nu_correct comes from there) Bruce On Tue, 19 Oct 2004, Joongnam Yang wrote: > Hi, > > I use

Re: [Freesurfer] MNI auto talairaching

I've got an error message when I was running "mri_vol2surf" file mri/transforms/talairach.xfm not found I guesss I need to do talairach transform, Could someone please tell me how to do it? Nam. ___ Freesurfer mailing list [EMAIL PROTECTED] https://m

Re: [Freesurfer] MNI auto talairaching

>>> Doug Greve <[EMAIL PROTECTED]> 10/29/04 2:16 PM >>> In general, you should not need a talairach transform to run mri_vol2surf, but I can't tell what you're trying to do -- no command-line :(. If you need to talairach, then you can run: recon-all -s subjectid

[Freesurfer] what the qsurfer can show

I ran qsurfer -stat thresh_zstat1 -subject ID -hemi lh -old and got the image displayed. But the image is structural image only. I thought that the above command shows the anatomical and functional data overlaid. Am I wrong? Or how can I see the two data overlaid in one image? Thanks in advance

[Freesurfer] Re: mri_vol2surf error

Thanks Doug, I am having trouble doing functional overlay with structural, either with GUI or command-line. On GUI, I open "structural" and "functional" directories in "csurf", but the overlay option under "File" doesn't show the overlay. I chose *.w file for the overlay data. Question1: Shou

[Freesurfer] Re: mri_vol2surf warning

Hi Doub, When I ran recon-all -stage1 -subjid ID I got the following error. Would someone give me any suggestion? It complains about Stratup.pm at the beginning and later it complains it can't locate the file?? Any comment would be appreciated ===

[Freesurfer] functional overlay

Hi all, If someone can give me help, it would be greately appreciated. in csurf GUI, I choose "New Functional", and I give it a name. (1) The name is entirely new for analysis or is it the directory that contains functional scan. If I give it a name, it asks for "Now, locate the single subjec

Re: [Freesurfer] functional overlay

Hi Bruce, I co-registered functional and structural images using SPM, the results of which looked normal. Then, I used spmmat2register to produce register.dat file. But "register.dat" contained only following two lines. subjectname 0.3000 It is supposed to have 8 lines. Could you guess what we

Re: [Freesurfer] functional overlay

Thanks Doug, When I run tkregister2 --targ structuralimage --mov functionalimage --reg register.dat I got the following error. == target volume X.img movable volume XX.img reg file register.dat LoadVol1 $Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 gr

Re: [Freesurfer] functional overlay

Thanks Doug, So, "structural data registration" "functional data registration" "co-registration" have to be done separately? How do I do the first two? The manual is pretty murky on that. Please enlighten me... I am trying to do functional overlay using csurf and there are so many hidden things w

[Freesurfer] convert functional into bfloat

Hi everyone, Is there a Freesurfer command to convert ANALYZE format functional data into *.bfloat? (I am trying to do functional overlay) Something like, xxx functionaldata.img *.bfloat Or do I have to use FSL Feat to get all the thresh_zstat*.img files using mri_convert command? Thanks

[Freesurfer] functional combo box

Hi everyone, For functional overlay, In csurf GUI window, on the right-most side, there is a "functional" combo box, where you are to set two items "session" and "scandir". Would someone tell what I am supposed to type in for th

Re: [Freesurfer] functional combo box

When I clicked "Volume-Stats" button on the top right corner of the window that shows up after I clicked "View Functional Data" button of csurf, I got the tksurfer window, but with the following error Error: Parsing command line options Option -invphaseflag not recognized This option was not recog

[Freesurfer] functional overlay looks right or wrong?

Thanks, Bruce. When I did successfully using csurf and tkmedit (I will try tksurfer later, though), I saw functional data overlaid onto structural data. Question: I was expecting some activated regions for my retinotopy data, but all I see is a large green or red contours. Is this what freesurfe

[Freesurfer] Re: functional overlay looks right or wrong?

Hi Bruce, We used stimuli of concentric rings whose radii expanded from trial to trial. We wanted to get retinotopic map using fMRI. So, we got structural data and functional scans. (We did the FSL Feat analysis and got stats results) We want to see the retinotopic map corresponding to the stimul

[Freesurfer] Tksurfer Overlay not working

Hi Bruce, I used Tksurfer to overlay fuctional onto anatomical. On the Load->Overlay window, I did indicate the functional *.bfloat and register.dat, but in the "Field" at the bottom, "Overlay layer 1 (empty)" is shown (inside "Field", all layers are empty). I guess that something is wrong. (Shou

[Freesurfer] Error: Overlay layer 1 (empty)

Hi All, I've got "Overlay Layer 1(empty)" when I opened TkSurfer to do funcitonal overlay. Is something wrong? Here is what I did. open csurf set functional directory. open tksurfer using "flattened" surface. open load-->overlay. The last line gives me a window at the bottom of which there is

[Freesurfer] csurf version?

Hi all, SessionTools menu in my csurf has only one submenu "View Functional Data". In some web sources that I read, there are many other submenus under it, such as "Setup Align/Funct Scans", "Calculate 3D Fourier Stats", etc. Is this version of csurf OLD? This freesurfer was installed last August

[Freesurfer] functional data not showing up

Hi All, I hope someone can locate the problem for me. Here is what I did. 1. clicked for "flattened" surface on csurf, which opens tksurfer (I see a flattened surface window) 2. clicked "load overlay" on tksurfer, which asks two inputs. For "Load overlay", I typed in XXX for XXX_000.bfloat

[Freesurfer] load overlay in TkSurfer

The "Load Overlay" window in TkSurfer is not working for me. The window has two fileds to fill in, "Load Overlay" and "User Registration". What's strange is that whatever I type in those two fields, TkSurfer doesn't complain. For example, if I type in "hello" and "abc.dat" literally for those two f

Re: [Freesurfer] load overlay in TkSurfer

The following is in .xdebug_tksurfer. Segfault xDebug stack (length: 1) 00: 00: Segfault Does it ring a bell, Bruce? Nam.

Re: [Freesurfer] load overlay in TkSurfer

Hi Bruce, I found the error messages in SUBJECTID/scripts/csurf.log The error was that there is no talairach.xfm in /mri/transorms directory. I though that using tkregister2 for co-registration would be enough. Would you let me know how to generate talairach.xfm? Nam. __

Re: [Freesurfer] load overlay in TkSurfer

Thanks, Kevin So, I guess there is nothing special about retinotopy data, but the functionl overlay that I got doesn't look right. (not much activation) Here is the two steps that I've done for the functional data before I overlay it onto anatomical data. Any comments are appreciated. 1. use "

[Freesurfer] mri_vol2surf warning seems serious

Hi, I would appreciate any comment on the following warning when I ran mri_vol2surf. At the end there is a warning, which might be serious. I ran lh and rh separately, and no warning message was issued for lh and the following warning was only issued for rh. . . . Done Mapping Source Volum

[Freesurfer] mri_vol2surf *.mat not found

For the mri_vol2surf, mri_vol2surf --src thresh_zstat1.img --src_type analyze --srcreg func2struc.dat --hemi lh --projfrac 0.5 --out ./thresh_zstat1-lh.w --out_type paint I got the following complaint. INFO: could not find XXX/XXX/thresh_zstat1.mat file for direction cosine info. Could someone

[Freesurfer] thresh_zstat1.img

Hi all, I did, (1) use mri_vol2surf to convert thresh_zstat*.img into thresh_zstat1-lh.w (2) use the *.w file to overlay it onto flattened surface. The resulting overlaid image (TkSurfer) doesn't show as much activation as that of thresh_zstat*.img (in FEAT). I see only a few tiny dots, not lar

Re: [Freesurfer] thresh_zstat1.img

Thanks, Kevin > Have you tried changing the threshold parameters, in the > View->Configure->Overlay dialog box? The manual is very coarse on that. I've tried various combinations of the three parameters there. If you know the rule of combination, Please let me know. Nam. _

Re: [Freesurfer] thresh_zstat1.img

> Did you visually check the registration of the functional to the structural? The registration using tkregister2 produces three files func2struc.mat func2struc.hdr func2struc.img, I've tried to load func2struc.hdr in TkSurfer, but it crashes. Again, I don't understand what you do when you "visua

Re: [Freesurfer] thresh_zstat1.img

Hi all, In TkSurfer, is there a way of saving *.w files (or any other images for that matter) into a printable format, so that I can print them out? Thanks. Nam. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/lis

[Freesurfer] make several into one

Hi all, I have 8 flattened overlay images (overlay between structural and functional images). Is there a way of combining those images into one image, so that each activation can have different colors in one image? Any comments would be apprecaited. Nam. _

[Freesurfer] from volume to surface

I have a functional volume, and a surface (occipital lobe cut, not the whole cortext) and I want to create *.w file using mri_vol2surf. mri_vol2surf gives me "segmentation fault", probably because the volume and the surface do not match. Could someone give me a clue on how to create a *.w file us

Re: [Freesurfer] from volume to surface

Sorry, Doug Here is the full command and log with segmentation fault. Nam. == mri_vol2surf --src FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --surf occip.patch.flat --out ./thresh_zstat1-lh.w --out_type paint I

Re: [Freesurfer] from volume to surface

Thanks, Doug, By any means, does the following register.dat look incorrect? subjid 3.80 5.00 0.15 1.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.00e+00 -1.525879e-05 0.00e+00 -1.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.0

Re: [Freesurfer] from volume to surface

Thanks, Doug, When you visually check the registration, using tkregister2 --s subjid --targ struc_fs_t1.img --mov YUNG070904_41.img --regheader --reg register.dat. two windows show up. Is there a source, or instructions, or manual, regarding what to do with the two winows? Nam. __

[Freesurfer] wmfill error

Hi all, During "create surface" on csurf, right after "fill white matter" is done, as soon as "tesselate RH white matter" starts, an error message comes up, which is images filled: somedirectory/mri/filled/COR-001...not found, wmfill first. I checked the directory of /mri/filled, which d

[Freesurfer] recon-all -stage1 error

Hi all, I ran recon-all -stage1 -subjid ID with the following errors. Any comment woud be appreciated. program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert

[Freesurfer] stage1 error

Hi, I got the following error message when I ran recon-all -stage1 -subjid ID Any comments appreciated. Nam. Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5

Re: [Freesurfer] wmfill error

lps, margaret On Wed, 22 Dec 2004, Joongnam Yang wrote: > Hi all, > > During "create surface" on csurf, > right after "fill white matter" is done, as soon as "tesselate RH white > matter" starts, > an error message comes up, which is > > imag

[Freesurfer] mni_perllib_0.07 installation error

Happy holidays for everyone! When I was installing mni_perllib_0.07, the following error messages keep popping out and at the end installation fails. batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at

[Freesurfer] fix topology

Hi happy new year everybody, "fix topology" in Freesurfer takes 57 hours on my machine, which has a speed of 1 GHz and RAM of 1 Gbytes, a pretty fast machine. 57 hours sounds TOO long for me; other processes take less than an hour. Does it sound OK, or something wrong? Any comments are apprecia

[Freesurfer] CC and pons

Hi all, recon-all -stage1 gives me an error on "could not find corpus callosum". So, I used Tkmedit to find xyz talairach coordinates of the two structures and ran stage1 again, many times with different coordinates. "surfaces" are twisted and "filled" volume didn't look like a brain. How can I f

[Freesurfer] unpredictable

Hi, For some subjects' data, pure Csurf GUI works, while for other subjects Csurf GUI complains, giving errors during "create surface", upon which I have to run the command-line option "recon-all -stage1" with CC and pons coordinates. Is it ture, I mean the Csurf GUI is unpredictable, because of

[Freesurfer] not symmetrical

Hi, For another subject, the inflated surfaces for left and right are not right after "create surface" in csurf GUI. They are not symmetrically cut. The brain seems to have been cut not through the midline, but a notch toward left hemisphere. When I looked at wm or T1 surfaces, they show that t

[Freesurfer] two questions

Hi, Sounds like trivial questions... (1) How do you check if the talairach.xfm is OK? (2) Either during the command-line option of recon-all -stage 1 thru 4, when do you use tkregister2 for registeration? Thanks for the help. Nam. ___ Freesurfer mail

[Freesurfer] 3dvolreg motion correction

Hi, The man page shows the following for the AFNI motion correction binary. 3dvolreg [options] dataset Registers each 3D sub-brick from the input dataset to the base brick. 'dataset' may contain a sub-brick selector list. Would someone tell me how to specify "dataset"? Is it *.img or COR-* or a

[Freesurfer] mri_convert

Hi, After I ran mri_convert, I saw the "orig" volumes. Are the red crosses in the image significant in that the center cross should be the center of the brain in terms of left and right hemispheres? It is not in the center, much away from the center in my "orig" volumes. If it has to be corrected

[Freesurfer] normalization failed

Hi, During recon-all -stage1 running, I got the following error. ... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status - Any suggestion would be appreciated. Na

Re: [Freesurfer] normalization failed

gt; 01/06/05 4:55 PM >>> check the talairach transform On Thu, 6 Jan 2005, Joongnam Yang wrote: > Hi, > > During recon-all -stage1 running, I got the following error. > > ... > MRInormalize: could not find any valid peaks > No such file or directory > mri_normalize: nor

Re: [Freesurfer] normalization failed

Hi, For one subject's data, "process volume" didn't get the skull stripped. The skull was there intact in "brain" volumes. To correct it, I used "expert preferences" and used "don't use watershed analyze", which led to most of the skull removed in "brain" volumes. But still there are pieces of th

[Freesurfer] pons-xyz

Thanks Bruce and Brian, When voxel dimensions are less than 1.75, "create surface" went smoothly. Question: The pons is still attached, I want to use -pons-xyz X Y Z TkMedit shows only RAS. (1) How can I have talairach coords shown up on TkMedit (2) RAS and Talairach coords are different, but

Re: [Freesurfer] normalization failed

Hi, I am having trouble removing the pons with recon-all -stage1 -pons-xyz. I've tried five pons coords, unsuccessfully. When you move the mouse location in the sagittal, horizontal, and coronal images, the slice numbers change. When I get the talairach coords for the pons, should the slice numbe

[Freesurfer] talairach coords on TkMedit

Hi, TkMedit doesn't show talairach coordinates. I ran talairach2 -s subjid, and clicked (View->Information->talairach), but still talairach coords row comes out blank in TkMedit, no numbers, just 0,0,0. Would someone suggest anything to make the tal coords available o nTkMedit? Thanks. Nam. _

Re: [Freesurfer] two questions

Hi, I collected new anatomical data with isometric voxels. When I ran "create surface," the pons is not being removed. I tried many different coordinates for the pons (either Volume Index or Talairach), but the pons is still not being cut out. Any suggestions? Thanks Nam. __

Re: [Freesurfer] two questions

t, you need to use volume scanner coords as input (you can turn them on under view->information). Make sure it is a point in which the pons appears disconnected in a horizontal view, and superior to the cerebellar peduncles. Bruce On Wed, 12 Jan 2005, Joongnam Yang wrote: > Hi, > &g

[Freesurfer] Each of the 256 slices?

t work? If not, you need to use > volume scanner coords as input (you can turn them on under > view->information). Make sure it is a point in which the pons appears > disconnected in a horizontal view, and superior to the cerebellar > peduncles. > > Bruce > > &g

[Freesurfer] manual editting not implemented

Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong?

Re: [Freesurfer] manual editting not implemented

interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005,

[Freesurfer] full surface cuts

Hi, I followed the manual instructions on full surface cuts, but not working. Here is what I did. (1) cut five relaxation cuts. (2) right-click. (3) left-click one of regions that are to be kept. (4) select "Fill Uncut Area" button, The image refrehses, but no change is made on the image. The circ

[Freesurfer] average of functional overlays across subjects

Hi All, Would someone point me to a place where I can get information on averaging of functional overlays across subjects? All the materials I have do not have any information about averaging Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] overlay of multiple *.w files onto the same surface

Hi, I know how to overlay a *.w file with a surface. Is it possible to overlay multiple *.w files onto the same surface on TkSurfer? If so, would someone let me know how to do it? Thanks. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] overlay of multiple *.w files onto the same surface

>>> Bruce Fischl <[EMAIL PROTECTED]> 01/27/05 1:17 PM >>> you can load multiple w files into different overlay layers in tksurfer, then switch between them in view->overlay layer cheers, Bruce On Thu, 27 Jan 2005, Joongnam Yang wrote: > Hi, > > I know ho

[Freesurfer] talairaching functional data

Hi, I ran "func2tal" with functional data (*.img) and got INFO: autodetected functype raw ERROR: only selxavg, selavg, and sfa functypes are currently supported How can I change *.img functional data into the above functypes? Thanks. Nam. ___ Freesu

Re: [Freesurfer] talairaching functional data

better off using mri_vol2vol. There are lots of docs with --help, including how to convert a volume into talairach space. doug Joongnam Yang wrote: > > Hi, > > I ran "func2tal" with functional data (*.img) and got > > INFO: autodetected functype raw > ERROR: onl

[Freesurfer] mri_convert

Hi I tried to convert *.img functional data into *.mnc file, using "mri_convert" and when I checked the *.mnc file for functional using "mincinfo", it gave me some "unknowns" for the time dimension. image: signed__ short 0 to 1131 image dimensions: xspace yspace zspace time dimension name

Re: [Freesurfer] Dicom

Hi all, I am sorry, since I might have missed the answer. My question is, the following question by Mr. Ajay Pillai has been answered? If yes, would someone forward me the answer please? Thanks. Nam. >>> Ajay Pillai <[EMAIL PROTECTED]> 04/27/05 2:26 PM >>> Hi, I am trying to convert my dicom fu

Re: [Freesurfer] Dicom

ere is no special naming requirements -- in fact the file names can be random). The output will be f001.{img,hdr,mat} f002.{img,hdr,mat} doug Joongnam Yang wrote: > > Hi all, > > I am sorry, since I might have missed the answer. > My question is, the following question by Mr.

Re: [Freesurfer] Dicom

IL PROTECTED]> 04/28/05 6:09 PM >>> It will transform all of them that belong to the same series into one file. If they don't all belong to the same series, then you're on your own. doug Joongnam Yang wrote: > > Thanks Doug, > > Is there a way of transforming

[Freesurfer] occipital cuts

Hi all, The freesurfer manual on occipital cuts is clear on where to cut, but does anyone have experience on where to cut, so that the flattening of the cut would look reasonable and consistent? I've tried several cuts, but whenever I tried it, the flattened surfaces look different and it is not s

답신: Re: [Freesurfer] occipital cuts

of cortex, Anders, Marty and Roger et al. typically made one planar cut to cut off the posterior 1/3, then one cut down the fundus of the calcarine all the way anterior. cheers, Bruce On Tue, 10 May 2005, Joongnam Yang wrote: > Hi all, > > The freesurfer manual on occipital cuts is cl

[Freesurfer] flattening with "folded" brain cuts

Hi all, Freesurfer allows occipital cuts of "inflated" brain to be flattened. Is it possible to flatten occipital cuts of "folded" brain? Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] BRIK and tkregister

Hi, I am using an old version of Freesurfer where retinotopy-analysis is enabled. If anyone having such experience, please help me. I am having trouble with csurf, and here is what I did. (1) changed Analyze file (*.hdr, *.img) into *.BRIK and *.HEAD using to3d (2) in csurf, under "session

[Freesurfer] occipatal cuts

Hi all, I did the occipital cut for the right brain and flattened it. When I opened it with Tksurfer of csurf, the flattened surface showed up on the right edge of the display window of Tksurfer, instead of being in the center of the window. (The left flattened surface came out in the center, and

[Freesurfer] how do you include parietal lobe in the cut?

Hi, I know how to cut the occipital lobe and flatten it. You cut calcarine and pick three points and another point to select the plane and do "cut plane". Would someone let me know how to extend the cut so that the cut can include part of the parietal lobe? The menu bar has "whole brain cut" and

Re: [Freesurfer] Cerebellum atlas

If it is in progress, it means that it is not usable by end-users yet? If so, when would the how-to guide be available? (This would be a wonderful tool for my project in which I need to see a particular region labeled, i.e., lateral portion of the areas between parietal and occipital lobes. I am

[Freesurfer] activation levels of each voxel

Hi all, When I overlay functional data (e.g. from FSL) onto a Freesurfer-produced inflated brain, I see the activations shown in colors. I want to pick a voxel in Talairach coordinates in those activations and see how the particular voxel's activation level changes throughout different data sets o

Re: Re: [Freesurfer] activation levels of each voxel

Thanks for the answer, > If you want to create statistical maps in surface space, then use > mris_preproc to assemble the data. Then use one of the FSL tools to > do stats or use mri_glmfit Where could I get mris_preproc and mri_glmfit? Google displays nothing on those two functions.^_^ > Yo

[Freesurfer] two functions location

Hi, "mris_preproc" and "mri_glmfit" These two functions are not included in the version of Freesurfer that I have. Does anyone know where I can get them? Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma