Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

convert DK atlas ROI to .nii.gz in MNI space
by Yang, Daniel 18 Jul '13

18 Jul '13

Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz. However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space? Many thanks!! Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Re: [Freesurfer] Loading thickness data in python
by Sebastian Urchs 17 Jul '13

17 Jul '13

Hi Satra, thank you very much - this has been tremendously helpful. I have now identfied neighbouring verteces within a certain distance using networkx and all_pairs_dijkstra_path_length. I would now like to create my own curvature overlay (similar to the thickness file) by assigning non-zero values to neighboring verteces to a selected vertex and zero to others. My question is: is there any way I can save a numpy array to a "morphometric" file using nibabel or a different package? Thank you very much, Sebastian On 15 July 2013 15:58, Satrajit Ghosh <satra(a)mit.edu> wrote: > hi sebastian, > > you simply need to read the geometry file and the morphometry vector and > the two pieces will give you what you need. > > the geometry file gives you the relation between vertex indices via the > faces array. > > ``` > def return_neighbors(faces, vertex_index): > faces_containing_vertex = np.nonzero((faces == > vertex_index).sum(axis=1))[0] > neighbors = np.setdiff(faces[faces_containg_vertex, :].flatten(), > vertex_index) > return neighbors > ``` > > cheers, > > satra > > On Mon, Jul 15, 2013 at 9:52 AM, Sebastian Urchs < > sebastian.urchs(a)gmail.com> wrote: > >> Hi Satra, >> >> thank you very much. I believe I have to rephrase my question as I didn't >> completely think it through. I need to find neighboring vertices to a >> specified vertex and then read out their thickness values. I don't think I >> can do this directly from the morphometry vector that pysurfer gives me. >> >> Thanks again, I'll send another mail to the mailinglist. >> >> Best, >> Sebastian >> >> >> On 15 July 2013 15:22, Satrajit Ghosh <satra(a)mit.edu> wrote: >> >>> hi sebastian, >>> >>> please take a look at pysurfer (https://github.com/nipy/pysurfer) and >>> nibabel (https://github.com/nipy/nibabel) >>> >>> the relevant code is here: >>> >>> https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py >>> >>> cheers, >>> >>> satra >>> >>> On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs < >>> sebastian.urchs(a)gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I am trying to figure out how to load thickness data into python such >>>> that I would be able to identify the thickness at a given mesh node and >>>> also identify surrounding nodes. I searched the mailinglist and found this >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but >>>> this unfortunately did not solve my question as I was unable to find a >>>> downloadable version of pymgh. >>>> >>>> Is there some python package that you could point me to and that allows >>>> me to load thickness data and do analysis in python? >>>> >>>> Thanks in advance! >>>> Sebastian >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >> >

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Re: [Freesurfer] Tracula problem in pre-processing
by Anastasia Yendiki 17 Jul '13

17 Jul '13

Yes. Does the file $FREESURFER_HOME/bin/flirt.fsl exist? On Tue, 16 Jul 2013, Gundran, Andrew wrote: > I've been doing that but I still get that same error... > > source $FREESURFER_HOME/SetUpFreeSurfer.csh right? > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Tuesday, July 16, 2013 4:42 PM > To: Gundran, Andrew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Tracula problem in pre-processing > > > You're very welcome. The error is for flirt.fsl, which is a copy of flirt included in the freesurfer distribution. So if you want to use that, you'll need to source the freesurfer setup script as usual. (You wouldn't need to if you were using flirt from the fsl distribution.) > > On Tue, 16 Jul 2013, Gundran, Andrew wrote: > >> And that worked. Great news...another error this time with FSL's flirt. I'm a bit confused on that one since I use FSL a bit within a terminal. I didnt think I had to setenv for it? >> >> flirt.fsl -ref >> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb >> register.34704/fslregister/refvol.fslregister.nii -in >> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb >> register.34704/fslregister/movvol.fslregister.nii -bins 256 -cost >> corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 >> -verbose 0 -omat >> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb >> register.34704/fslregister/fslmat0.trans.mat -schedule >> /usr/local/fsl/etc/flirtsch/xyztrans.sch -init >> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb >> register.34704/reg.init.dat.fsl.mat0 >> flirt.fsl: Command not found. >> ERROR: flirt >> >> >> Thanks so much for your patience! >> >> ________________________________________ >> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: Tuesday, July 16, 2013 11:28 AM >> To: Gundran, Andrew >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] Tracula problem in pre-processing >> >> Hi Andrew - Try installing XQuartz: >> http://xquartz.macosforge.org/landing/ >> >> a.y >> >> On Mon, 15 Jul 2013, Gundran, Andrew wrote: >> >>> build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >>> ________________________________________ >>> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >>> Sent: Monday, July 15, 2013 5:20 PM >>> To: Gundran, Andrew >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] Tracula problem in pre-processing >>> >>> Can you please check for a line that says "build-stamp" in the log >>> that tells you which freesurfer build you used? >>> >>> On Mon, 15 Jul 2013, Gundran, Andrew wrote: >>> >>>> From the log I found this >>>> >>>> Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version >>>> 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>> >>>> >>>> And mac osx 10.6.8 >>>> ________________________________________ >>>> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >>>> Sent: Monday, July 15, 2013 4:51 PM >>>> To: Gundran, Andrew >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>> Subject: RE: [Freesurfer] Tracula problem in pre-processing >>>> >>>> Can you tell us which build of freesurfer you're using (should be in >>>> trac-all.log) and what version of OSX you have this installed in? >>>> >>>> On Mon, 15 Jul 2013, Gundran, Andrew wrote: >>>> >>>>> Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else? >>>>> >>>>> fslswapdim >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an >>>>> at_orig.nii.gz x z -y >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an >>>>> at.nii.gz fslorient -forceradiological >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an >>>>> at.nii.gz >>>>> tkregister2 --mov >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an >>>>> at_orig.nii.gz --targ >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an >>>>> at.nii.gz --regheader --noedit --fslregout >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/ana >>>>> torig2anat.mat --reg >>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/ana >>>>> t2anatorig.dat >>>>> dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced >>>>> from: /Applications/freesurfer//tktools/tkregister2.bin >>>>> Reason: image not found >>>>> Trace/BPT trap >>>>> ________________________________________ >>>>> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >>>>> Sent: Monday, July 15, 2013 4:19 PM >>>>> To: Gundran, Andrew >>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>> Subject: RE: [Freesurfer] Tracula problem in pre-processing >>>>> >>>>> Hi Andrew - The files should be one row per DWI volume. See example >>>>> here, under "Specify the diffusion-encoding gradient table" and >>>>> "Specify the b-value table": >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>>> >>>>> Hope this helps, >>>>> a.y >>>>> >>>>> On Mon, 15 Jul 2013, Gundran, Andrew wrote: >>>>> >>>>>> I attached the file above. >>>>>> >>>>>> For the configuration problem, I actually just installed >>>>>> freesurfer onto one of our newer macs and it seemed to work fine. >>>>>> I was running it on an older linux version of freesurfer. Still >>>>>> couldnt figure the issue on the linux though for the config file. >>>>>> ________________________________________ >>>>>> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >>>>>> Sent: Monday, July 15, 2013 12:35 PM >>>>>> To: Gundran, Andrew >>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Subject: Re: [Freesurfer] Tracula problem in pre-processing >>>>>> >>>>>> Hi Andrew - My guess is that it's something about the file >>>>>> dmri/dwi_orig.mghdti.bvals that's causing the error. Could you >>>>>> please send along that file? >>>>>> >>>>>> Also, how did you fix your previous configuration file problem? >>>>>> Letting the list know about the resolution of the issue would help >>>>>> other users, who may have the same issue in the future and search the list archives. >>>>>> It'll also help me figure out if there are any checks I could add >>>>>> to trac-all to preclude this. >>>>>> >>>>>> Thanks! >>>>>> a.y >>>>>> >>>>>> On Tue, 9 Jul 2013, Gundran, Andrew wrote: >>>>>> >>>>>>> Helo all, >>>>>>> >>>>>>> I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file. >>>>>>> >>>>>>> ln -sf >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.ni >>>>>>> i.gz >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.n >>>>>>> ii.gz >>>>>>> awk: can't open file 1000 >>>>>>> source line number 1 >>>>>>> mri_concat --i >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr >>>>>>> ame.nii.gz --mean --o >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.n >>>>>>> ii.gz >>>>>>> niiRead(): error opening file >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr >>>>>>> ame.nii.gz >>>>>>> ninputs = 1 >>>>>>> Checking inputs >>>>>>> ERROR: reading >>>>>>> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr >>>>>>> ame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin >>>>>>> Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>>>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>>>>> >>>>>>> >>>>>>> I have also attached the trac-all log. >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is addressed. If you believe this e-mail was sent to you >>>>>> in error and the e-mail contains patient information, please >>>>>> contact the Partners Compliance HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>> you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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Re: [Freesurfer] Artefactual skull stripping for some subjects
by Tudor Popescu 17 Jul '13

17 Jul '13

Hi again, I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions! Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu <tudor3(a)gmail.com> wrote: > Thanks Bruce. So the massive chunks that appear as missing in freeview, > e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces > don't exist there. If I mouse above that area, brainmask.mgz intensities > (which seem to be always identical to T1.mgz ones) seem quite normal to me, > i.e. they're not all 0 but vary in a range centred around ~100. > > As for the segmentation (aseg) - not quite sure where I need to look for > that. I attach here the main volumes & surfaces of this subject. Could my > "-wsthresh 35" recon not have replaced the existing one? > > Many thanks again! > Tudor > > PS: why does freeview show the coordinates in the order [x z y] instead of > [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle > coordinate to decrease, rather than the third one. > > PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to > do with conformity and intensity correction, just like the difference > between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would > be a binary image (a mask consisting of 0s and 1s), rather than a regular > (skull-stripped) structural. > > > On 11 July 2013 21:40, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Tudor >> >> can you cc the list so others can answer? What are the intensities in the >> excluded right temporal wm in the brainmask.mgz? What is the aseg like >> there? Looks like an intensity normalization failure, but I'm not sure why. >> If you want to upload the subject I'll take a look >> Bruce >> >> On Thu, 11 Jul 2013, Tudor Popescu wrote: >> >> Hi Bruce, >>> >>> Sorry, wasn't sure whether you'd seen my previous message. So in the >>> meantime, after the following command for subject C06 (whose artefactual >>> skull strip I previously included as a screenshot) completed without >>> error, >>> >>> recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06 >>> >>> ..the volumes&surfaces still look bad (see screenshot and recon log >>> attached). >>> >>> C06 is just one of several subjects for which this has happened. Is there >>> anything else I can try? Thanks! >>> >>> Tudor >>> >>> On 9 July 2013 13:33, Tudor Popescu <tudor3(a)gmail.com> wrote: >>> Thanks for clarifying this Doug! >>> >>> Please let me know if anyone has suggestions about my other >>> questions below, re skull stripping. >>> >>> Cheers! >>> T >>> >>> On 8 July 2013 18:01, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz >>> >>> If you only have one run, then 001 and raw are the >>> same >>> orig.mgz is the first conformed volume >>> >>> doug >>> >>> >>> >>> On 07/08/2013 12:38 PM, Tudor Popescu wrote: >>> > Thanks Bruce. I have looked at that part of the >>> wiki but I was >>> > wondering whether the screenshots at all suggest >>> that all artefacts >>> > are likely to be the result of the same problem, >>> and that e.g. >>> > re-running recon for all subjects with a >>> watershed>25 and with the >>> > -no-wsgcaatlas flag might be the thing to do in >>> this case, rather than >>> > manually editing slices in tkmedit. >>> > >>> > So after making these corrections to all affected >>> subjects, before >>> > proceeding to analyses, is a visual inspection in >>> freeview of the >>> > brain.mgz of all subjects enough? It seems like >>> some of these >>> > skull-stripping errors are quite subtle and can be >>> easily missed (as I >>> > have, in fact, when I checked the output after my >>> first recon-all). >>> > >>> > the T1.mgz is intensity corrected and >>> conformed (the orig.mgz is >>> > just conformed). >>> > >>> > So are both derived from 001.mgz? Otherwise, what >>> is the difference >>> > between 001.mgz and orig.mgz? >>> > >>> > Thanks! >>> > Tudor >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> The information in this e-mail is intended only for the person >>> to whom it is >>> addressed. If you believe this e-mail was sent to you in error >>> and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent >>> to you in error >>> but does not contain patient information, please contact the >>> sender and properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> >

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beta weights from FS-Fast analysis
by Joseph Dien 17 Jul '13

17 Jul '13

I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? Sorry for all the questions! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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Freesurfer installation
by pablo najt 17 Jul '13

17 Jul '13

Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup But after the installations when I open the terminal nothing happens. I also tried to launch freesurfer this way: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If I do this I get: command not found command not found command not found Any advice on how to finally set up the software would be great help. Thank you in anticipation.Pablo

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Re: [Freesurfer] Button Press Regressor
by Douglas N Greve 17 Jul '13

17 Jul '13

It looks like it is the 1st regressor. Although there appears to be a period of time where this is no button press. If the button press is the only event, then it is definitely the 1st regressor. Note that all runs are concatenated together. doug On 07/16/2013 12:17 PM, Nicholas Paul Denisuk wrote: > Freesurfer Users, > > Here is the X.mat file. Thank you! > > Nick Denisuk > > On 7/16/13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> can you send the X.mat file? >> >> >> On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote: >>> Dear Freesurfer Users, >>> >>> I have opened up the X.mat file from the analysis. I think that the >>> button regressor is the third column in the file, but I am not 100% >>> sure. Do you know which column the button regressor is? Below is the >>> background info to this question. >>> >>> >>>>> I am trying to regress out the activity associated with button presses >>> in my GLM analysis. How do I generate a nuisance regressor file >>> analogous to a white matter regressor generated in functional >>> connectivity (a one column time course file)? >>> >>> Thanks you, >>> >>> Nick >>> >>> >>>>> Hi Nick, please remember to post to the list and not to us personally. >>> To answer your question, you could create an run an analysis with just >>> the button press. Go into the analysis and get the button press >>> regressor from X.mat, then save it as a text file in the run folder. >>> Then make your analysis and specify this as a task regressor. I >>> *think* that should work. >>> >>> doug >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Gray matter missed in the pial layer after mri_segment
by Erin Browning 17 Jul '13

17 Jul '13

Hello-- We have a set of scans with bad artifact throughout the temporal lobe and the superior cortex. We've had to do the normalization steps (n3 correction, normalization) manually on most of these scans to preserve the gm/wm boundary. Now, when we run mri_segment, it leaves out some gray matter along the pial border. Is there a correction for this? Mri_segment has wlo and whi and ghi, but no glo, and it doesn't look like there's a method to add gray matter to the pial boundary like there is to remove it. Thank you, Erin Browning

2 1

Q) Medial_wall.label
by Yune Lee 17 Jul '13

17 Jul '13

Hello freesurfer experts, For visualization purpose (i.e., displaying group maps), I applied a mask for medial wall regions using the files (e.g., rh.Medial_wall.label or lh.Medial.wall.label), which I found in fsaverage/label/ directory. However, I noticed a somewhat imperfect medial wall masking in both hemispheres, such that transversing lines are seen in unthresholded t maps for both hemispheres (see attached ). Those lines eventually disappear when I increased threshold, but I wonder why this happened. Any ideas? best, yune

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Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all
by Knut J Bjuland 17 Jul '13

17 Jul '13

Hi, I have some trouble running recon-all longitudinal pipelines. When recon-all comes to mri_register_ca it crashes without giving a message, even tough 8g ram was available. I have run the program with -debug. Is there any other option I may use? The system is running Rocks 6.0 (Mamba), and it uses Slurm queue system. Can I use the FreeSurfer 5.3 longitudinal process with data processed with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed effects model MATLAB tools. Knut J

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