[Freesurfer] mri_probedicom

Is there a way to get mri_probedicom to let you scroll through dicom images instead of viewing each image slice by slice? If not, is there something else available with freesurfer that will allow you to look at the dicom images? -Keyma ___ Freesurfer

Re: [Freesurfer] overview of motion correction

s the transform, correct? In which case you YOU> can do it anytime. YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > Would you recommend using this command on the orig volume before I start YOU> the YOU> > rest of the proce

Re: [Freesurfer] overview of motion correction

ch is a wrapper Doug YOU> wrote to use FLIRT. It works quite well, and writes out a transform (and YOU> transforms the volume if you want). YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > I would like to take 3 different scan vo

[Freesurfer] overview of motion correction

I would like to take 3 different scan volumes of the same subject and compare their parcellation values. I want to make sure that motion between the scans will not change the parcellation values. Is mri_motion_correct the proper tool to use for aligning the scans before proceeding with the processi

[Freesurfer] mri_motion_correct

Can you use mri_motion_correct to align orig volumes from 2 different scans without averaging the volumes in the output? -Keyma ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] SaveSegmentation problem fixed in tkmedit

I downloaded this file and when I try to run tkmedit I get the following error: tkmedit -f TFL_3006_6/mri/T1/ Couldn't find tkm_common.tcl: Not in % freesurfer/subjects> I checked to make sure that the tkm_common.tcl file was in the $FREESURFER_HOME/lib/tcl/ and it was in the correct location. w

Re: [Freesurfer] mri_normalize error

Thanks the -no1d flag worked. What does this flag change about the normalization process? -Keyma Quoting Bruce Fischl <[EMAIL PROTECTED]>: YOU> run it with -no1d. Also, check the talairach. YOU> YOU> Bruce YOU> YOU> On Mon, 26 Jul 2004, Chekema YOU> Nayasha Prince wrote: YOU> YOU> > Hello,

Re: [Freesurfer] mri_normalize error

ion failed No such file or directory Quoting Evelina Busa <[EMAIL PROTECTED]>: YOU> Hi Keyma! YOU> YOU> Could you send the command you used, and possibly more output? (say, the YOU> YOU> last 15 lines before the error message?) YOU> YOU> Thanks! YOU> YOU>

[Freesurfer] mri_normalize error

Hello, I'm trying to normalize an MPRAGE dataset and I received the following message from the mri_normalize: MRInormalize:could not find any valid peaks no such file or directory mri_normalize: normalization failed no such file or directory I tried to set control points ( 4 of them specifically

Re: [Freesurfer] new segmentation error

dical Imaging YOU> Bldg. 149, 13th Street, CNY 2301 YOU> Charlestown, MA 02129 YOU> YOU> On Wed, 14 Jul 2004, Chekema Nayasha Prince wrote: YOU> YOU> > I used the new segmentation in tkmedit to draw labels in the orig YOU> volume. When I YOU> > went to "

[Freesurfer] new segmentation error

I used the new segmentation in tkmedit to draw labels in the orig volume. When I went to "File-> Save segmentation As" and tried to same it in a new directory I got the following error: "Error:Invalid Command Name "Save Segmentation"" Is there another way to save the segmentation volume? -Keyma

[Freesurfer] moving a label in tkmedit

Can you move a label to a new location that has already been drawn in tkmedit without redrawing the label ? -Keyma ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] drawing labels in tkmedit

i'm using the "Select Voxels Tool" to make labels in tkemdit. Each time I draw a label I save it and I have to close tkmedit it and open it again to save a new label. Is there another way to draw all the labels at the same time and save them under different names? -Keyma

[Freesurfer] mri_cor2label

I would like to create a label in the orig volume and copy this label to the another scan of the same subject in order to measure SNR values. I drew the label using tkmedit on the orig volume and saved it. Is mri_cor2label the correct function to use in order to copy this label to the other scan?

[Freesurfer] (no subject)

I am trying to load the thickness overlay on the inflated brain but when I select the h.thickness surface it doesn't overlay anything. The inflated brain just refreshes but no overlay appear. Is there another way to get the overlay loaded? -Keyma ___ Fr

[Freesurfer] Parcellate_subject

I ran parcellate subject and I overlayed the annotation on the inflated surface. The medial wall segmentation looks incorrect. The medial wall area section is very large and is also spreading into the frontal regions. I looked at the T1 image with the lh.white surface loaded in tkmedit and the outl

[Freesurfer] segmentation fault with mprph_subject

Hello, I received the following segmentation fault when I ran morph_subject: mris2rgb -o hr_MPRAGE_040623/.reg -both -c /home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/lh.sulc -canon /home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/

[Freesurfer] SNR values

Is it possible to get SNR values from freesurfer for regions of the brain? -Keyma ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Signal to Noise Values

Is there a way to get the SNR values from a region in the brain through tkmedit? or even a contrast to noise value? -Keyma ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer