Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

visualization after cluster correction
by Jacobs H (NP) 16 May '11

16 May '11

Hi FreeSurfers, This is more a visualization question. I did the cortical thickness analyses on my data and compared my two groups statistically. After that I ran the mri_glmfit-sim to correct for multiple comparisons using the cluster correction. When I visualize the results, each cluster has its own color. However, I would like to present the original sig.mgh file (where each vertex has received a significance value according to the color table) minus the clusters that did not survive the correction. How should I do that? Thank you very much! Best regards Heidi [cid:327214308@11052011-0AC8] Heidi Jacobs, MSc. PhD student Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Alzheimer Center Limburg Division Cognitive Neuropsychiatry and Clinical Neurosciences h.jacobs(a)maastrichtuniversity.nl <mailto:h.jacobs@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 Note: the email addresses have changed! [cid:327214308@11052011-0ACF] Please consider your environmental responsibility before printing this e-mail.

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.mgh to .label ??
by Ritobrato Datta 16 May '11

16 May '11

Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri

2 1

surfsace of specific broadman's area
by Oya, Hiroyuki (UI Health Care) 15 May '11

15 May '11

Dear all, I like to create a surface rendering restricted to some area (selected from aparc.annot.a2009s.ctab files)? Any suggestion would be appreciated. Best, Hiroyuki ________________________________ 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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creating roi
by 李俏俊 13 May '11

13 May '11

dear all, i want to get ROI in the naive space (for example STG) using freesurfer,i check the email list and find that command mri_extract_label may help, so i try it as follow, mri_extract_label aparc+aseg.mgz 1030 outli.mgz but i do not get the ROI i expect. do anyone know how can i get the ROI in naive space ？by other commands?by other software? many thanks~ qjli -- best wishes -------------------------------------------------- CCM计算医学中心 www.ccm.org.cn 中国科学院自动化研究所 Institute of Automation, Chinese Academy of Sciences --------------------------------------------------

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Cerebellum segmentation, auto vs manual reference?
by McLean John (NHS Greater Glasgow & Clyde) 13 May '11

13 May '11

Hi, I've found some volume differences in the cerebellum between two groups I've been studying. I used freesurfer v4.5 to do the segmentation. I am looking for a reference to justify the use of Freesurfer and to say that it compares well with manual tracing of the cerebellum but I'm struggling to find a paper with that data. Can anyone comment or point me in the right direction? The Fischl et al 2002 Neuron paper has a comparison of most subcortical regions but doesn't include the cerebellum and other papers I've seen by Makris et al 03' and 05' looks to employ a more involved and detailed approach for the cerebellum rather than only running Freesurfer's recon-all process. Many Thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Re: [Freesurfer] Pial surface error
by Allie Rosen 13 May '11

13 May '11

Hi Mario, I'm not sure what an N4 correction is, but the Freesurfer team helped me to solve the problem. Here are their instructions: Sometimes when the skullstrip is wrong, it affects the surfaces even if the wm parcellation is correct. I ran -skullstrip with the watershed parameter of 30, and then reran the subject with -autorecon2 -autorecon3. You can find info how how to run watershed here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix>I hope this helps! I can send over our full conversation if this doesn't give you the information you need. Allie On Fri, May 13, 2011 at 4:26 PM, Mario Ortega <mario.ortega(a)gmail.com>wrote: > HI Allie, > I am having this exact issue, and I was able to fix only a few of them, Did > the Freesurfer team ever give you a reliable fix? I used an N4 correction > before the entire FS process. > -Mario > > > On Wed, Apr 20, 2011 at 8:32 AM, Allie Rosen <rosen.allie(a)gmail.com>wrote: > >> Hi, >> >> Do you want me to email you in a few days about this? >> >> Allie >> >> >> >> >> On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu>wrote: >> >>> Got it. I'll look at it and get back to you. >>> >>> >>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>>> >>>> http://dl.dropbox.com/u/14127241/C42.tar.gz >>>> >>>> Here is the link to the subject. I hope this works!! >>>> >>>> Allie >>>> >>>> >>>> >>>> On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu >>>> >wrote: >>>> >>>> Another way you can try is upload it to your google doc account and >>>>> send me >>>>> the link. Someone did that before. >>>>> >>>>> >>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>> >>>>> Hi, >>>>> >>>>>> >>>>>> No, I'm not from the centre. I'm working on putting the files in >>>>>> Dropbox >>>>>> and >>>>>> sending you a link to them, because apparently I don't have ftp >>>>>> access. >>>>>> >>>>>> Allie >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen < >>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>> >>>>>>> wrote: >>>>>>> >>>>>> >>>>>> Are you from the center? If so you can just cd into /space/outgoing >>>>>> and >>>>>> >>>>>>> copy your file there. If not, you can follow the instructions in the >>>>>>> box >>>>>>> at >>>>>>> the top using a terminal. >>>>>>> >>>>>>> >>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> >>>>>>>> I'm really sorry, but I don't understand those instructions. Do I >>>>>>>> login >>>>>>>> to >>>>>>>> the freesurfer website? Or do I login through a terminal somehow? Do >>>>>>>> I >>>>>>>> type >>>>>>>> the stuff in the boxes into the terminal? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Allie >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen < >>>>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>> Hi Allie, >>>>>>>> >>>>>>>> >>>>>>>>> You can compress the subject dir and upload it following the >>>>>>>>> instructions >>>>>>>>> here >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>> >>>>>>>>> Hi Khoa, >>>>>>>>> >>>>>>>>> >>>>>>>>> How do I upload subjects? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Allie >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen < >>>>>>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Allie, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Can you upload the subject? I'll take a look and see if I can >>>>>>>>>>> figure >>>>>>>>>>> out >>>>>>>>>>> what's wrong. >>>>>>>>>>> >>>>>>>>>>> -Khoa >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> This (recon-all after wm.mgz and brainmask.mgz edits) didn't >>>>>>>>>>> work. >>>>>>>>>>> >>>>>>>>>>>> The >>>>>>>>>>>> part >>>>>>>>>>>> that wasn't included in the pial or white matter surfaces is >>>>>>>>>>>> still >>>>>>>>>>>> not >>>>>>>>>>>> included. The intensities in the white matter regions are no >>>>>>>>>>>> different >>>>>>>>>>>> than >>>>>>>>>>>> in white matter regions that were included in the white matter. >>>>>>>>>>>> Any >>>>>>>>>>>> other >>>>>>>>>>>> suggestions? >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Allie >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen < >>>>>>>>>>>> rosen.allie(a)gmail.com >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I am running recon-all tonight using wm voxels that I manually >>>>>>>>>>>> >>>>>>>>>>>>> added >>>>>>>>>>>>> (I >>>>>>>>>>>>> also edited brainmask.mgz to add missing grey matter). To me it >>>>>>>>>>>>> doesn't >>>>>>>>>>>>> really look like a case of the white matter not having a high >>>>>>>>>>>>> enough >>>>>>>>>>>>> intensity. It simply looks like the whole lobe was ignored, >>>>>>>>>>>>> regardless >>>>>>>>>>>>> of >>>>>>>>>>>>> intensity. But I'll check tomorrow to see if the intensity is >>>>>>>>>>>>> low. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Allie >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl < >>>>>>>>>>>>> fischl(a)nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> What is the intensity of the white matter in the regions you >>>>>>>>>>>>> drew >>>>>>>>>>>>> in? >>>>>>>>>>>>> A >>>>>>>>>>>>> >>>>>>>>>>>>> couple of control points might help if it is less than 110 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Apr 18, 2011, at 12:36 PM, Allie Rosen < >>>>>>>>>>>>>> rosen.allie(a)gmail.com> >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for all the responses! I've actually had the same >>>>>>>>>>>>>> problem >>>>>>>>>>>>>> for >>>>>>>>>>>>>> multiple subjects. I'm using version 5.0.0. I'll try fixing >>>>>>>>>>>>>> the >>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>> as well. I've attached pictures of where I am adding wm >>>>>>>>>>>>>> voxels. >>>>>>>>>>>>>> They >>>>>>>>>>>>>> aren't >>>>>>>>>>>>>> really in the same places as in the online tutorials. Could >>>>>>>>>>>>>> you >>>>>>>>>>>>>> take >>>>>>>>>>>>>> a >>>>>>>>>>>>>> quick >>>>>>>>>>>>>> look to see if they're in the right place? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Allie >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori << >>>>>>>>>>>>>> sita(a)nmr.mgh.harvard.edu> >>>>>>>>>>>>>> sita(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> pial surface which looks like this can only be corrected by >>>>>>>>>>>>>>> correcting >>>>>>>>>>>>>>> the wm.mgz. Also I would suggest to try and fix the >>>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> see >>>>>>>>>>>>>>> if it >>>>>>>>>>>>>>> corrects the surfaces as well. Since part of the cerebellum >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> stripped >>>>>>>>>>>>>>> off, >>>>>>>>>>>>>>> it's probably affecting the segmentation as well but I could >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> wrong. >>>>>>>>>>>>>>> what >>>>>>>>>>>>>>> version of freesurfer are you using. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Can I still add voxels to wm.mgz even though the points >>>>>>>>>>>>>>> would be >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> outside >>>>>>>>>>>>>>>> even the pial boundary? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> Allie >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>>>>>>>>>>>>>>> < <sita(a)nmr.mgh.harvard.edu>sita(a)nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> This probably needs white matter edits but it's hard to >>>>>>>>>>>>>>>> tell >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>> slice. Please refer to our white matter edits wiki and >>>>>>>>>>>>>>>>> toplogical >>>>>>>>>>>>>>>>> defects >>>>>>>>>>>>>>>>> wiki and see if it helps in fixing the errors in your >>>>>>>>>>>>>>>>> datasets. >>>>>>>>>>>>>>>>> Also >>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>> looks like part of the Cerebellum is stripped off. You >>>>>>>>>>>>>>>>> might >>>>>>>>>>>>>>>>> want >>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> correct >>>>>>>>>>>>>>>>> that as well. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Once processed, several of my subjects have had errors >>>>>>>>>>>>>>>>> around >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> occipital >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lobe. Attached is an example. I've already tried editing >>>>>>>>>>>>>>>>>> brainmask.mgz >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> running recon-all, but as you can see, this didn't change >>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>> pial >>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>> wm >>>>>>>>>>>>>>>>>> borders. What can I do to fix this? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Allie Rosen, MSc Candidate >>>>>>>>>>>>>>>>>> Graduate Student, Department of Neurosurgery >>>>>>>>>>>>>>>>>> Toronto Western Hospital 14-327 >>>>>>>>>>>>>>>>>> 399 Bathurst St. >>>>>>>>>>>>>>>>>> University of Toronto >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> <2.png> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> <3.png> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>> >> >> _______________________________________________ >> 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] Temporal lobe tracing abnomality uncorrected by control points
by Bruce Fischl 13 May '11

13 May '11

Hi Ammar, if you adjust control points you should be running autorecon2-cp not -wm. cheers Bruce On Fri, 13 May 2011, Moiyadi, Ammar wrote: > Hi I attached the log file for this subject. I tried adjusting control points and performing autorecon2-wm in repeated iterations. It helped a little but I still am missing a large chunk of both gray and white temporal matter. I'm not sure how many iterations it will take to get a complete tracing but it doesn't seem to be helping as much as the initial few runs. > > Ammar Moiyadi, BS > Professional Research Assistant > Psychiatry, School of Medicine > 303-724-5490 > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Tuesday, May 10, 2011 6:01 PM > To: Moiyadi, Ammar > Subject: RE: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points > > can you send us the recon-all.log file for that subject? And make sure to > cc the list on your replies so others can help! > > Bruce > On Tue, 10 May 2011, > Moiyadi, Ammar wrote: > >> Hi Bruce - The image is of the brainmask.mgz file. I have attached another image showing the wm.mgz file - you're right, the wm regions where I placed the control groups is very dark if not absent. I still don't understand why the proper gray matter boundaries were not obtained however. I did run autorecon2-wm after adding the control points but I will run it again just in case. >> >> Thanks for your help, >> >> Ammar >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Tuesday, May 10, 2011 2:34 PM >> To: Moiyadi, Ammar >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points >> >> what image are you displaying in this png? If it is one of the brain*.mgz >> then your control points aren't working as the wm is still very dark where >> you place them. Did you run autorecon2-wm after putting the control points >> in? >> >> On Tue, 10 May 2011, Moiyadi, >> Ammar wrote: >> >>> Dear Freesurfers, >>> >>> Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before. >>> >>> Your input is much appreciated! >>> >>> Ammar >>> >> >> >> 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. >> >> >

1 0

display results on fsaverage / calculate area
by Boris Bernhardt 13 May '11

13 May '11

Hello Freesurfer-experts, I just analyzed some FreeSurfer cortical thickness data that have been surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). For the visualization and reporting of my findings, I have a two questions: 1. Is there anything that conceptually speaks against showing my results on non-inflated surfaces of fsaverage, such as the white matter surface, the pial surface, or even a mid-surface model? 2. I have a couple of ROIs defined on the surface of fsaverage and want to report the surface area of a given ROI in mm^2. Should I calculate the area of a ROI directly from the given surface of fsaverage, or to take the area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which represent the averages of the individuals that went into fsaverage. I am asking because I was slightly unclear of the wiki-instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface suggests to use ?h.pial.avg.area.mgh; on the other hand, the more recently edited http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage says that "The surface area of the new average subject (fsaverage) is that of a typical subject" I am using freesurfer 4.5.0. Hope my questions make sense and thank you very much for answering them, Boris --- Boris Bernhardt, PhD Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, 04103 Leipzig, Germany p: +(49) 341 9940 2658 e: bernhardt(a)cbs.mpg.de http://www.cbs.mpg.de/~bernhardt

6 10

comparing FS version 4.0 and FS versione 5.2
by irene.mat＠libero.it 13 May '11

13 May '11

Hi all, I'm performing a follow-up longitudinal study in a group of patients. I have 2 brain MRIs per patient (T0 and T1 after 4 years). I'd like to know if I can analyse the T0 MRI with FS version 4.0 and compare these results with T1 MRI analyzed with FS version 5.2. Thanks, Irene Mattisi University Hospital of Padova, Italy.

3 2

recon-all - problem with corRead(): can't open file */COR-.info
by Vanessa Lim 12 May '11

12 May '11

Hi, I have files from Siemen's Skyra which I have used MRI_Convert to nii I have tried using just the dicom files as well as changing the files to *.nii.gz but I still get the error corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ I get files in G2 but there is nothing in the mri/orig I am following http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction as I am completely new to freesurfer. I'm using a virtual machine on Vista; Ubantu. Many thanks! Regards, Vanessa Error below: FreeSurfer:~/apps/freesurfer/subjects/GrossNii> recon-all -i ~/apps/freesurfer/subjects/SPARSEG -subjid G2 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/virtualuser/apps/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/apps/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/apps/freesurfer/subjects/G2 mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/virtualuser/apps/freesurfer/subjects/SPARSEG... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

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