Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] tksurfer & rtview
by Michelle Umali 17 Aug '11

17 Aug '11

Hi Doug, Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data? The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings. I used 5mm smoothing. Thank you very much, Michelle Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > The activation looks pretty reasonable. As you point out, the angles > are a mess. How did you set the color scale for the angles? You should > leave it as a heat scale (if you're using tksurfer-sess). How much did > you smooth? > > doug > > Michelle Umali wrote: >> Hi Doug, >> Attached is a pic of the significance and angle maps for polar and eccen. >> >> What do you think? >> >> Thanks. >> Michelle >> >> Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >> >>> what does the activation look like? Does it look right? Can you send a pic? >>> doug >>> >>> Michelle Umali wrote: >>>> Hi Doug, >>>> The z-values are consistently near or greater than 4. It just >>>> seems that the >>>> visualization of the angles is somehow incorrect... >>>> >>>> Is there be anything else that I need to check? >>>> >>>> Thanks. >>>> Michelle >>>> _______________________________________________ >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> 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. >> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ----- End forwarded message -----

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DOSS or DODS
by Tetiana Dadakova 17 Aug '11

17 Aug '11

Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja.

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preproc-sess registration problem
by raij＠nmr.mgh.harvard.edu 16 Aug '11

16 Aug '11

Hi Doug, We have an old EPI data set where automatic (preproc-sess) or bbregister with any init type give a bad result. Hence, we are attempting to use a manual register.dat file instead. However, we must be doing something wrong, because changing preproc-sess to use our manual register.dat (done a couple of years ago) seems to have no effect. I suspect our preproc-sess options as not set up correctly. Our goal is to present the results on fsaverage surface. Our preproc-sess command line is as follows: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat The whole analysis script is at /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh FS version = 5.1 machine = adapt (analysis running on cluster) setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ individual subject = avml07 surface analysis lhrh, results to be presented on fsaverage surface Total of 3 runs per analysis (each with different number of TRs) Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) FIR analysis Thank you for the advice in advance! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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mri_convert generates different mgz from nii and nii.gz
by Forrest Sheng Bao 16 Aug '11

16 Aug '11

hi there, i noticed a strange problem tonight. I had a .nii.gz file. I used mri_convert to convert it into a .mgz file. I also used gzip to unzip the .nii.gz file and then used mri_convert again to get another .mgz file. But the two .mgz files have different md5 sums. Does anyone know what caused the problem? Or is there a problem? Cheers, Forrest

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Abnormal segmentation of hippocampal subfields
by New Fei Ho 16 Aug '11

16 Aug '11

Hi, I've been inspecting the hippocampal subfield segmentation in my subjects. So far, the subfields segmentation appear to be consistent across my images. 1. Is there any criterion used in defining proper subfield segmentation (any landmarks I should look out during QC)? 2. What are the corrective measures when the subfield segmentation fails? I attach examples of 2 subjects that have two T1-weighted scans taken in tandem in the same session (of which one two images appears to have malfunctioned segmentation) Thanks, Newfei

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Saving annotation and stats after expand boundary of region
by Keefe, Helen L 16 Aug '11

16 Aug '11

Hi Bruce, Doug, and All, I have corrected a boundary between lh corpuscallosum and caudalanteriorcingulate. I have overwritten the label/lh.aparc.annot as per Bruce's email below. However, doesn't this leave a number of files with incorrect information now in the stats directory? Do I need to rerun something to bring these up to date? Thanks, Helen ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, July 11, 2011 2:57 PM To: Keefe, Helen L Subject: RE: [Freesurfer] save label after expand boundary of region sure. Good luck Bruce On Mon, 11 Jul 2011, Keefe, Helen L wrote: > Thank you! > > This will help me clear up a lot of problem scans - I really appreciate your help > > Helen > > > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Monday, July 11, 2011 2:42 PM > To: Keefe, Helen L > Subject: RE: [Freesurfer] save label after expand boundary of region > > no, it won't matter > On Mon, 11 Jul 2011, Keefe, Helen L wrote: > >> Hi Bruce - >> >> I made the edits on the pial surface using command: >> >> >> tksurfer $i lh pial -annotation aparc >> >> >> Does that make any difference? Since the instructions say to use the inflated surface: >> >> tksurfer -annot aparc subjectid rh inflated >> >> Thanks, >> Helen >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Monday, July 11, 2011 11:31 AM >> To: Keefe, Helen L >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] save label after expand boundary of region >> >> if you export it as an annotation then all the labels will be combined in >> one file. I think you are probably editing the ?h.aparc.annot, so you could >> overwrite that one if you want. The correct mri_segstats command could then >> be found in the subject's recon-all.log or recon-all.cmd file in the >> scripts dir. >> >> cheers >> Bruce >> >> >> On Mon, 11 Jul 2011, Keefe, Helen L wrote: >> >>> Hi Bruce, Doug, and All: >>> >>> Questions on a continuing problem: >>> >>> When I run tksurfer, the caudalanteriorcingulate is invaded by the corpuscallosum. >>> I edited the boundary using the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit >>> >>> I'm then instructed to "Save the annotation: File > Label > Export Annotation. Probably choose a new name rather than writing over an existing file" >>> >>> I don't need a new name - I just need to save the labels for the caudalanteriorcingulate and the corpuscallosum, which both now look correct. How/where >>> do I do that? Here are the files in the label dir: >>> >>> lh.cortex.label >>> lh.aparc.annot >>> lh.aparc.a2009s.annot >>> rh.cortex.label >>> rh.aparc.annot >>> aparc.annot.ctab >>> rh.aparc.a2009s.annot >>> aparc.annot.a2009s.ctab >>> >>> >>> Also - >>> >>> I previously asked what I need to do after that to ensure accurate measurements. >>> Bruce responded, >>> "I don't think you need recon2 since you are just changing the aparc. I believe you can just run the aparc stats step, but I'll cc Doug who might know >>> better." >>> >>> Any advice on all this? >>> >>> Thanks, >>> Helen >>> >>> >>> __________________________________________________________________________________________________________________________________________________________ >>> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential >>> and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying >>> of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >>> >>> __________________________________________________________________________________________________________________________________________________________ >>> >>> >> >> >> 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. >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >> ________________________________ >> >> >> > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ > > > ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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automated brodmann parcellation
by Corey Keller 16 Aug '11

16 Aug '11

Hi Freesurfers, I was wondering if you have come across a method to automatically parcellate the whole brain into Brodmann areas. I know the newest freesurfer version does this for several BAs but not all BAs have been incorporated. I was wondering if anyone knows of an existing Brodmann atlas (for example from Micron, AFNI, FSL, WFU_PickAtlas) that I can download and apply to my subjects' surfaces in freesurfer via mri_vol2surf? Thanks in advance. Best, Corey

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Re: [Freesurfer] QDEC - generate stats data table error: cannot find /usr/local
by Jamaan Alghamdi 16 Aug '11

16 Aug '11

Hi Rajeev, Usually, this type of error is produced if stats file is missed, check if aseg. stats file is there in directory "/usr/local/freesurfer/subjects/140/stats" directory. If this file is missed in some subjects, you can add "--skip" to command line like; asegstats2table --subjects 01 02 03 .... --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile ....... Jamaan Jamaan Alghamdi 07779801950 0151 795 4627 Magnetic Resonance & Image Analysis Research Centre (MARIARC) University of Liverpool Pembroke place Liverpool L69 3GE http://web.mac.com/jamaan/Jamaan/Welcome.html http://www.easyneuroimaging.com/

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Intracranial volume
by carolina.mr 16 Aug '11

16 Aug '11

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preproc-sess - cannot find AFNI command 3dvolreg
by Adam Nitenson 16 Aug '11

16 Aug '11

Hi Doug and Freesurfers, I encountered an error during preproc-sess (Stable 5) that I have never seen before: ERROR: cannot find AFNI command 3dvolreg The commands I entered were: setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd $SUBJECTS_DIR preproc-sess -s MTH20100AA -fwhm 5 -per-run I've run this set of commands many times without this problem, so did something change or am I missing something simple? Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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