[Freesurfer] automating tkmedit

bar of my terminal reads "terminal - tkmedit.bin". When I type "echo $PATH" I get the respone that the PATH variable does not exist. Does anyone know how to make the command function in tkmedit? Thanks, Jared Price Center for Neurological Imaging Brigham and Women&#x

[Freesurfer] "psubmit: Command not found" error

Hi everybody, this is Jared over at the Brigham. Quick question for anyone who knows. I am trying to rebuild a subcortical atlas using the script rebuild_gca_atlas.csh. When calling the script I almost immediately get the error "psubmit: Command not found." I would like to get this working b

[Freesurfer] correction

Hi, this is Jared again at the Brigham. Quick correction. The error says "pbsubmit: Command not found." not "psubmit: Command not found." Thanks -Jared Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Str

[Freesurfer] automating tkmedit

Hi everybody, I had a quick question I was hoping someone could help me out with. I am trying to automate a few aspects of tkmedit but am running into some trouble in creating a shell script that can control it. Under normal circumstances, for example, the first line would be something like

[Freesurfer] longitudinal processing

Hi everybody, 2 quick questions about longitudinal processing. 1) does the longitudinal processing even call the default gca atlas or does it use something else? 2) when processing say 7 time points should all longitudinal scans be processed from baseline or should time 3 be processed from

[Freesurfer] volumetric analysis with different versions

Hi freesurfer gurus, I just noticed that version 4.1.0 is out. We have a relatively large amount of data already processed through various freesurfer versions such as 4.0.0 4.0.2 4.0.5. Is it valid to compare volumetric measurements from the subcortical segmentation file aseg.mgz across thes

[Freesurfer] shell choice

Hello freesurfer gurus, I noticed on the wiki that they recommend using tcsh when running freesurfer, although they say other shells can be used. Is there a significant advantage to using tcsh when running freesurfer? If I would rather use bash is there any significant reason not to? Warmest

[Freesurfer] missing information in volume headers

Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the orig.mgz volumes the values listed for echo time and flip angle in some of the scans were 0.00, even though there was a listing for repetition time. What could have c

[Freesurfer] quick follow-up

Will missing header info affect the rebuild_gca_atlas script? I noticed it didn't like it if echo time, repetition time etc. didn't match. Also, I assume there is no difference, or minimal enough difference to ignore, in the 001.mgz file when converted from say nifti or straight from dicom.

[Freesurfer] fixing segmentation errors

Hello freesurfers! We have a large data set which has segmentation volumes that have been manually labeled. Along the way occasionally a voxel which should have been labeled as left-hemisphere was labeled with the corresponding right-hemisphere label. For example, there might be a few voxels

[Freesurfer] mri_convert

Hi everybody, We have a set of patients who were all run using the same freesurfer version, except that some of the patients had their dicom files converted to 001.mgz with a somewhat older version of freesurfer. For example some of them went through that step with version 4.0 or 4.0.2 or 4.0

[Freesurfer] mri_convert

Hi everyone, I have a quick question but an important one. We are working on a 5 year study involving well over 1000 scans. Processing of these patients is primarily done using a cluster machine loaded with freesurfer version x86_64-redhat-linux-gnu-dev4-20080904. However, sometimes it is us

[Freesurfer] mri_convert

correction to the previous message (which is below). The Macs in the local lab are now running Darwin-leopard-i686-stable 4.1.0 and the version of mri_convert on that seems to be 1.146.2.3 Hi everyone, I have a quick question but an important one. We are working on a 5 year study involvi

[Freesurfer] volume changes

Dear gurus, when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial space we are seeing some significant volume changes in the segmentation. Anyone know why or how to fix it. Jared __

[Freesurfer] freesurfer dice coefficient calculation

Hi freesurfer masters, Quick question on the way freesurfer calculates the dice coefficient. I am interested in getting an INTERsubject dice coefficient as a measure of similarity between 2 subjects. My question is, do I need to do an INTERsubject registration step before calculating the dice

[Freesurfer] Brain segmentation stats

Gurus, Looking over some stats recently I noticed that if you add up all of the freesurfer stats for ventricles, namely the left and right lateral ventricles plus 3rd, 4th, and 5th ventricles and subtract that from the "Number of Brain Segmentation Voxels" stat, you do not get the value of the

[Freesurfer] mean symmetric surface distance, Hausdorff distance etc..

Hi freesurfer masters, I was wondering if freesurfer had a way of comparing two segmentations for surface differences, something along the lines of a Hausdorff distance or the symmetric mean absolute surface distance Cheers, Jared ___ Freesurfer maili

[Freesurfer] follow-up to Hausdorff distance question

Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that could calculate it, but I don't see it in the /Applications/freesurfer/bin directory. Is it elsewhere? Is it included with 4.4.0? ___

[Freesurfer] Hausdorff distance

Hi gurus, I am evaluating two segmentation routines relative to a gold standard and would like to calculate the Hausdorff distance for each routine relative to the gold standard in the left and right Amygdala, Caudate, Putamen, and Hippocampus. I know that there are 3 main options to the mri_

[Freesurfer] modifying dicom headers

Hi all, I am looking for a powerful, robust tool for modifying dicom headers that can be called from the command-line and scripted. For example, I may need to alter the subject ID with which a dicom study was uploaded. We are managing a multi-site study and the various sites do not always upl

[Freesurfer] frontal gray and white matter volumes

Hi all, I am interested in obtain a total gray matter volume and a total white matter volume specific to the frontal lobes. How can this be done in freesurfer? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

[Freesurfer] registration of gene expression images

Hi all, I have some images (2-d (single slice)) from mouse brains which show gene expression data from in-situ hybridization from several different mice. I would like to align each of these images with one another. Does anyone know of a really good tool for that sort of thing? Ideally I am l

[Freesurfer] frontal gray matter and frontal white matter volumes

Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of

[Freesurfer] wiki page on how to read the stats files?

Hi all, Does anyone know if there is a detailed wiki page on how to interpret each of the different stats files. To this point I have primarily used the aseg.stats file but one of the PIs we are working with wants a measure of total gray matter and total white matter specific to the frontal lo

[Freesurfer] qcache

Hi all, This should be a quick question to answer. I recently ran "recon-all -s -qcache" on a group of subjects after they had undergone initial processing. This was done using something of the form "for subjvar in `ls`; do recon-all -s $subjvar -qcache; done" (actually this was done on a gr

[Freesurfer] extracting single structures from aseg.mgz

Anyone know how to extract a single structure from aseg.mgz? In other words I assume it is possible to use the information in aseg.mgz to extract a single structure such that there is a new.mgz file that contains just the segmentation of the putamen or just of the caudate or whatever. Thanks.

[Freesurfer] follow-up

Thanks, I tried mri_extract_label and it works fine. However, it extracts the structure and gives it the label "nerve". Is there any way within mri_extract_label to keep the original labels (i.e. left putamen, right putamen, or whatever)? Jared ___

[Freesurfer] manually segment with 001.mgz as main volume?

Hi all, I want to do a manual segmentation of the putamen in tkmedit, but rather than using brainmask.mgz as the main volume, I wanted to use 001.mgz. This is because the intensity normalization step can in certain cases brighten lighter areas of the putamen to 110. Anyway, when I load the 00

[Freesurfer] reply

I guess I am not entirely sure what the contrast properties of orig.mgz are. After looking at the recon-all DevTable I don't see anything that explicitly mentions any intensity normalization occurring before this point so I imagine it would work. I guess I will just ask you for your suggesti

[Freesurfer] reply

Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz --regheader -o ...This created a volume but the same issue remained. When I load a segmentation on top of the created volume, tkmedit won't let me alter the segmentation. If I use "new segmentation" as opposed to load

[Freesurfer] follow-up

...Also, I should mention that slice thickness in the MRI acquisition sequence was 1.3 mm so the native voxels are not 1x1x1. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] moving 001.mgz to anatomical space

I see the mistake I made. Works well now. Thanks for the help. Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] registration to a template

Hi all, Does anyone have any recommendations for testing anatomical similarity between 2 different subjects? Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_robust_register

Hi gurus, The output of mri_robust_register includes some instruction for checking the registration. In my case the ouput said I could check the registration by running "tkregister2 --mov 0110837_20090425/mri/001.anatomicalspace.mgz --targ 0311501_scan1_20061205/mri/001.anatomicalspace.mgz --lt

Re: [Freesurfer] qdec.table.dat

Hi Matt, I believe the problem lies in how excel treats end of line characters (even Excel for Mac). You could use Open-office which will export to a more Unix-friendly format, or you could try using tr (a Unix command-line utility that could change the problematic end of line characters to Unix-c

[Freesurfer] rebuild_gca_atlas.csh

Freesurfer gurus: When using rebuild_gca_atlas.csh it fails due to the fact that not all of the TRs TEs and FlipAngles are identical across all scans I am using for the atlas. Is there any major concern if we artificially change these values using mri_modify so that they are identical? Much tha

[Freesurfer] follow-up to automation of TkMedit

m a command prompt or can correct any missteps that I may have taken please let me know. Thanks and all the best to each of you, Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Street Boston, MA 02115