Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

question about atrophy and FS-FAST
by Mario Ortega 11 Nov '13

11 Nov '13

Hello Freesurfer group, I have a general question about the Freesurfer pipeline when applied to fMRI BOLD scans. In general, with heavily atrophied or older individuals, would there be no necessary corrections to make for atrophy due to the non-linear surface inflation transformation that is applied to every individual subject? I ask, as I we have atrophied subjects in our dataset and want to make sure a BOLD signal is comparable between tissues and subjects. Thanks

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aparcstats2table question
by Jonathan Holt 11 Nov '13

11 Nov '13

Hi FS experts, I’m about to run aparcstats2table for a longitudinal study, and I’m wondering seeing as I’ve already written a longitudinal qdec table that includes subject IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3 … etc AND the qdec to aparcstats2table or should I just pass the qdec? I only ask as the tutorial says -subjects is required, but it seems redundant and I wanted to verify. jon

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Re: [Freesurfer] bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 11 Nov '13

11 Nov '13

Hi Laura - First of all, which version of freesurfer do you have? It looks to me like you've based your config file on the old example file that came with version 5.1. Second, could you please convert your bvecs and bvals files to 3 columns and 1 column, respectively, then run trac-all and send the trac-all.log file that shows the errors that you get? Thanks! a.y On Mon, 11 Nov 2013, Laura Christine Anderson wrote: > Hi Anastasia, I am still struggling with this same error message, despite > having rearranged the bval and bvec files in many different configurations > (and making sure that each value in these files had the same number of > digits, which I am not sure even matters). I am attaching my most recent > bval and bvec files as well as the config file to see if you have any > advice. > > Thanks so much for your help! > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/15/13 11:17 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - This means that there is only 1 line in each of the files, so >> the end-of-line characters aren't recognized. I'd make sure that the file >> is saved as plain text. >> >> a.y >> >> On Tue, 15 Oct 2013, Laura Christine Anderson wrote: >> >>> When I run "wc -l" on the bvec and bval files, I get "1" for both. >>> Running >>> just "wc" gives "1 279 3312" for bvec and "1 93 456" for bval >>> >>> Laura C. Anderson, B.A. >>> Graduate Student >>> Clinical & Developmental Psychology >>> University of Maryland >>> College Park, MD 20742 >>> BPS 0112 >>> >>> >>> >>> >>> On 10/14/13 5:18 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> >>>> Hi Laura - I don't think the error "bvecs and bvals don't have the same >>>> number of entries" should have to do with interspersed zero b-values. >>>> When >>>> you run "wc -l" on the bvecs and bvals files, what do you get? >>>> >>>> a.y >>>> >>>> On Mon, 14 Oct 2013, Laura Christine Anderson wrote: >>>> >>>>> Hi Anastasia, the bval/bvec files were created on a Mac and not with >>>>> excel. I am not seeing the ^M character when I view the files in unix >>>>> with >>>>> the more command or in gedit perhaps when I sent you the files, >>>>> something >>>>> became corrupted? I am wondering if my issue has something to do with >>>>> the >>>>> fact that there are 3 sets of 30 rows with a b0 image before each of >>>>> the 3 >>>>> sets. In the examples I have seen, the b0 images all seem to be at the >>>>> beginning of the bvec and bval files. I am attaching a screenshot of >>>>> the >>>>> bvec and bval files as I see them in case that is helpful. If you >>>>> would >>>>> rather me send the actual files again, what is the best way to do that >>>>> without the formatting getting messed up? Before, I was using a free >>>>> fileshare program. >>>>> >>>>> Thank you! >>>>> Laura >>>>> >>>>> Laura C. Anderson, B.A. >>>>> Graduate Student >>>>> Clinical & Developmental Psychology >>>>> University of Maryland >>>>> College Park, MD 20742 >>>>> BPS 0112 >>>>> >>>>> >>>>> >>>>> >>>>> On 10/11/13 2:38 PM, "Anastasia Yendiki" >>>>> <ayendiki(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>>> >>>>>> Hi Laura - Were these bval/bvec files created on windows or with >>>>>> excel >>>>>> by >>>>>> any chance? When you view them in unix (with the more command for >>>>>> example) >>>>>> you'll see an "^M" character instead of every end-of-line. Can you >>>>>> try >>>>>> editing these files in a unix editor to fix that? Let me know if this >>>>>> solves the problem. >>>>>> >>>>>> a.y >>>>>> >>>>>> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >>>>>> >>>>>>> Hi Anastasia, >>>>>>> Thanks so much for your help! Attached are bvec, bval and >>>>>>> trac-all.log >>>>>>> files. >>>>>>> >>>>>>> I have been stuck at one of the preprocessing steps (trac all) for >>>>>>> some >>>>>>> time and keep getting the >>>>>>> error: bvecs and bvals don't have the same number of entries. I saw >>>>>>> a >>>>>>> couple blogs online about >>>>>>> this, but did not see any resolution. I am wondering if it is >>>>>>> because >>>>>>> the B0 images are >>>>>>> interspersed? (see attached bvec file). If you have any insight, I >>>>>>> would love some feedback >>>>>>> whenever you get the chance. >>>>>>> >>>>>>> Laura >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> 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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Files uploaded
by pietro de rossi 11 Nov '13

11 Nov '13

HI, I succesfully uploaded the files. Thanks in advance for your help! Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

1 0

recon all error
by Boric, Katica A. 11 Nov '13

11 Nov '13

Greetings Freesurfers! recon-all -s XXX_SurferOutput exited with ERRORS These are the errors in the log: Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 I would really appreciate any advice! Thank you very much, Katica

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Re: [Freesurfer] Longitudinal freesurfer analysis question
by Martin Reuter 11 Nov '13

11 Nov '13

Hi Salil, please send questions to the free surfer mailing list. If you used the longitudinal stream for processing the etiv should be the same in all time points. It is computed in the 'base' = within subject template once for the entire series. It seems that you did not run your images through the longitudinal stream if your etiv is different across time points. For longitudinal processing see here: http://freesurfer.net/fswiki/LongitudinalProcessing Bes,t Martin On Nov 10, 2013, at 3:37 PM, Salil Soman <salsoman(a)stanford.edu> wrote: > Dear Dr. Reuter, > > I have performed freesurfer 5.3 with hippo subfields Analysis on patients that have 2 consecutive scans (pre and post surgery). I have generated Segstats statistics for each individual time point. I have noticed the etiv is different on all of the cases for each time point (scan 1 is different from 2). This has led me to worry that it may not be legitimate to perform analyses of changes in volumes of structures by computing differences in values between time points). I am writing to inquire if you were familiar with /had an opinion regarding this matter. > > Best wishes, > > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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request
by pietro de rossi 11 Nov '13

11 Nov '13

Dear Freesurfers, I am working on the segmentation of mdeft structural images (Siemens Allegra 3T-acquired) of schizophrenia patients. I had troubles editing temporal regions (especially superior temporal gyrus) by adding control points. After re-running the image in the pipeline (autorecon2-cp) the problem on the STG was solved but the pial and white matter boundaries in the lower temporal regions were completely messed up. Could anyone take a look and tell me if the image is editable? I would like to upload the pre and post editing folders so that an expert can give me an opinion. Is this the correct link to upload files and folders? https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Sorry to bother you all but this would be extremely helpful given that I experienced a similar problem in several subjects of this sample. Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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Error in Config File
by Cherise R. Chin Fatt 11 Nov '13

11 Nov '13

Hello: I am trying to run two subjects using Tracula. I have created a config file, and getting the following error: set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects I have tried to debug and can't seem to find the source of this problem. My config file is as follows: setenv SUBJECTS_DIR /FreeSurfer_Reconstruction/All_Recons set dtroot = /FreeSurfer_Reconstruction/DTI_Raw set subjlist = (PID0001 \ PID0002) set dcmroot = /FreeSurfer_Reconstruction/DTI_Raw set dcmlist = (PID0001/orig/000031.DCM \ PID0002/orig/00001.dcm) Any help would be appreciated. Thank you, Cherise.

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Strange segmentation - what is going on?
by Erik Lindberg 11 Nov '13

11 Nov '13

Dear Freesufer experts, I attached an image that display really odd segmentation of a brain - I do not understand why this is happening - I got it in quite a lot of these from my last run of Freesufer - any suggestion on what is going on? Thanks Olof

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Etiv difference in difference in same patient
by Salil Soman 10 Nov '13

10 Nov '13

Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistically significant. As there was no change in their skulls between scans, I am having difficulty understanding how this is possible. Can anyone suggest what I may be doing wrong? Best wishes, Salil

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Freesurfer November 2013