Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 19 May '16

19 May '16

Hi Doug, No that’s not how I usually store my files- I have a folder for the particular study that I am working on then the dicoms for each subject in that study are stored in individual subject folders within the study folder. I got a chance to look around the recon-all logs this morning for a subject that I had successfully processed in the past (but that I get the error when I try to process this same dataset now). From comparing the recon-all log from when recon-all ran successfully versus now, things are running fine up until it gets to MRI_convert. However, it looks like things are actually starting to go haywire during MRI_convert even before I get the warning about the ASCII header and recon-all exits. It appears that MRI_convert is having some trouble with extracting some of the information it needs from the dicom file, resulting in the error that I posted. I know you guys are busy, but would you be able to take a look at the log files? I’ve only been using freesurfer a few weeks, so I would definitely appreciate any insights you might have from looking at the log files. Thank you! I don't have any idea what is going wrong. I noticed that the file that it is having problems with is here /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm Do you really keep all your dicom files in that location? On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > Hi Doug, > Sorry- I've added entire correspondence onto the end of this e-mail. I don't think the disk filled up as I am on a 3 TB hard drive and I still have ~2 TB of free space on my disk. Anything else you think it could be? > Thanks! > Joseph Aloi > Please remember to include previous correspondence otherwise we can't > keep track of the problem! > Eg, I don't have the previous email to see what the error was. Is it > possible that the disk filled up? > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > Hi Doug, > > > > Yes, you are correct- data I have previously processed without any > > problems is no longer being processed. > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > ago so I have not changed my freesurfer version recently. > > > > Thanks! > > > > Joseph Aloi > > Graduate Student, MD/PhD Scholars Program > > Department of Pharmacology and Experimental Neuroscience > > University of Nebraska Medical Center > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > > Boys Town National Research Hospital > So the exact same data set is now generating an error whereas it ran > smoothly before? What version of FS are you using? Did you change versions? > doug > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > Hi freesurfer experts, > > > > I have recently begun to use freesurfer to do structural MRI > > analyses. I have been able to successfully process about 40 > > structural scans with recon-all thus far, but starting a few days ago, > > I started getting this error whenever I run recon-all: > > > > WARNING: file > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > contain a Siemens ASCII header > > > > has this file been anonymized? > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016 > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > the cause of the error: > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > already successfully processed > > > > - - Re-run recon-all the same datasets but on a different computer > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > run recon-all > > > > > > For all of these steps, I have gotten the exact same error message. > > The files should be anonymized, since I used osirix’s “anonymize and > > convert” function to generate the dicom files (the scans were given to > > me as .ima files). > > > > Any suggestions on what to try next? > > > > Thank you! > > > > > > Joseph Aloi > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > 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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<file://localhost/transfer/outgoing/flat/greve> The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Re: [Freesurfer] WM Hyperintensities
by Elijah Mak 19 May '16

19 May '16

Hi Martin, I am also following this thread with interest. Is that multi-modal prototype you mentioned available in the next FS6.0? Many thanks. Best Wishes, Elijah Navena Rebecca Lingum <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 18 May 2016 10:25:09 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Would any member of the FreeSurfer team be able to help with this question? I would like to use the FreeSurfer software to delineate white matter hyperintensities. I have processed my T1 images using the recon-all command, and in the aseg.stat file there is a value for WM hypointensities. Is there an alternate stream/ FreeSurfer algorithm that exists for the processing of T2w FLAIR images for WM hyperintensities? Thanks, Navena ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Martin Reuter <mreu...(a)nmr.mgh.harvard.edu> Sent: May 17, 2016 1:32 PM To: Freesurfer support list Subject: [Freesurfer] WM Hyperintensities Hi Navena, I am the wrong person to answer questions about the WM lesion stream. I think the one that is available in FreeSurfer is only based on T1 images, but a prototype of a better stream exists, that can incorporate different modalities. Best, Martin P.S. Changed the subject, to reflect that this is not a longitudinal question any more. On 05/17/2016 12:37 PM, Navena Rebecca Lingum wrote: Dear Martin, Thank you kindly for your prompt response. I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere. As it stands, I am finding it difficult to understand the exact "pipeline" of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats? Any help on the matter is much appreciated! Kindly, Navena Lingum On May 16, 2016, at 4:24 PM, Martin Reuter <mreu...(a)nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu <mreu...(a)nmr.mgh.harvard.edu>>> wrote: Hi Navena, There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates. Best, Martin On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: Dear FreeSurfer experts, My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command? Navena Lingum _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <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 athttp://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 listFreesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 29
by Caroline Beelen 19 May '16

19 May '16

Dag Jolijn, Gegenereerd! En ik heb gezien dat nr 13136 wm_lh_g_temp_sup_plan_tempo ertussen staat! (output linux) :) Groetjes, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: dinsdag 17 mei 2016 22:50 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 147, Issue 29 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: 3T flag (Moeller, Sebastian) 2. Re: FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities (Navena Rebecca Lingum) 3. Re: ERROR: cannot unpack mosiacs without ASCII header (Douglas N Greve) 4. Re: wm parcellation (Douglas N Greve) 5. Re: Same coordinates for all labels (Douglas N Greve) 6. Re: segfault using brainstem module from dev version (Martin Reuter) 7. WM Hyperintensities (Martin Reuter) 8. errors in wm and pial boundaries (Corinna Bauer) 9. Re: errors in wm and pial boundaries (Bruce Fischl) 10. Question on Yeo 2015 cognitive atlas (Josh Gray) 11. Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill (gangli) 12. Freesurfer (Limachia, Gaurang (NIH/NINDS) [F]) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 May 2016 16:01:19 +0000 From: "Moeller, Sebastian" <sebastian.moeller1(a)rwth-aachen.de> Subject: Re: [Freesurfer] 3T flag To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DAAC6E30-68D8-4C96-A658-1CD19D6A79A7(a)rwth-aachen.de> Content-Type: text/plain; charset="utf-8" Hi Kasper, > On May 17, 2016, at 17:44 , Kasper Jessen <kasper_j(a)cnsr.dk> wrote: > > Thanks for the answers :-) > > Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong?" > > What is it that is probably wrong? I would be amazed if that rationale was a truthful description of the full physical basis for the changes in inhomogeneities; and to be on the safe side (I never even discussed this with a physicist) I declare that it is incomplete and hence ?wrong?. The last thing I want is to spread half-baked information as ground truth? Best Regards Sebastian > > Best regards, > Kasper > > 2016-05-17 14:48 GMT+02:00 Moeller, Sebastian <sebastian.moeller1(a)rwth-aachen.de>: > Hi Kasper, > > > > On May 17, 2016, at 10:05 , Kasper Jessen <kasper_j(a)cnsr.dk> wrote: > > > > I would like to know the following: > > > > a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas? > > b) what does the 3T-specific NU intensity correction parameters do differently than the standard? > > If I recall correctly this is based on http://www.sciencedirect.com/science/article/pii/S1053811909006703: > Improvement of brain segmentation accuracy by optimizing > non-uniformity correction using N3 > > Type Journal Article > Author Weili Zheng > Author Michael W. L. Chee > Author Vitali Zagorodnov > URL http://www.sciencedirect.com/science/article/pii/S1053811909006703 > Volume 48 > Issue 1 > Pages 73-83 > Publication NeuroImage > ISSN 1053-8119 > Date October 15, 2009 > Journal Abbr NeuroImage > > So most likely it reduces the N# smoothing distance from the default > 200 to 50 > > Here is the relevant part from recon-all (v5.3): > if ($DoNuIntensityCor3T) then > # params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper > # "Improvement of brain segmentation accuracy by optimizing > # non-uniformity correction using N3" > set NuIterations = 1; > set cmd = ($cmd --proto-iters 1000 --distance 50) > endif > > A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong? > > Best Regards > Sebastian > > > > > Best > > Kasper > > > > 2016-05-10 8:09 GMT+02:00 Kasper Jessen <kasper_j(a)cnsr.dk>: > > Dear FreeSurfer group, > > > > Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment. > > > > However, where can i find the documentation for the above? > > > > Best regards, > > Kasper > > > > > > > > > > > > -- > > Kasper Jessen, > > MD, PhD student > > Center for neuropsychiatric Schizophrenia Research (CNSR) Mental > > Health Centre Glostrup Nordre Ringvej 29-67 > > 2600 Glostrup > > Tlf.: 24430136 > > E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk > > _______________________________________________ > > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kasper Jessen, > MD, PhD student > Center for neuropsychiatric Schizophrenia Research (CNSR) Mental > Health Centre Glostrup Nordre Ringvej 29-67 > 2600 Glostrup > Tlf.: 24430136 > E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk > _______________________________________________ > 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. ------------------------------ Message: 2 Date: Tue, 17 May 2016 16:37:18 +0000 From: Navena Rebecca Lingum <nlingum(a)uwo.ca> Subject: Re: [Freesurfer] FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8950AD6C-3FCE-4AA1-AC22-67FEB8ADB675(a)uwo.ca> Content-Type: text/plain; charset="windows-1252" Dear Martin, Thank you kindly for your prompt response. I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere. As it stands, I am finding it difficult to understand the exact ?pipeline? of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats? Any help on the matter is much appreciated! Kindly, Navena Lingum On May 16, 2016, at 4:24 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> wrote: Hi Navena, There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates. Best, Martin On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: Dear FreeSurfer experts, My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command? Navena Lingum _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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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Defining ROI and Finding the Cortical Thickness
by Mahtab Farahbakhsh 19 May '16

19 May '16

Dear freeSurfer, I have problems with defining new labels for my brain scan or even of fsaverage. I need to define a new label (ROI) to be able to find the grey matter thickness for that specific region. My first problem is that when I define a new label on fsaverage, it does not save it for me and it gives me the following error: mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz, -1): could not open file /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not open label file /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label I intend to define a new label (ROI) on fsaverage and then use the mri_labe2label command to copy it on my desired structural MRI image. But it does not work for me. My second problem is that when I define a new label on my subject's MRI image and I run the mri_anatomical_stats with the label of my subject, it does not give me any output and this is what I get: bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh limiting computations to label anon/label/lh.test.label. reading volume /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz... reading input surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... reading input pial surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial... reading input white surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... and the error is that it could not find the file lh.test.label, however I can see it in the label folder. Please guide me with this issue. Best Regards, Mahtab.

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Neuroimaging position available
by Anders Martin Fjell 19 May '16

19 May '16

At the Research Group for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available position in neuroimaging for an excellent candidate, who will work with several projects on life-span development and aging, dementia and biomedical risk factors using different brain imaging modalities. Please find more info here: http://uio.easycruit.com/vacancy/1633291/65775?iso=no Interested candidates are welcome to contact me if they have questions. Best whishes, Anders M Fjell http://www.oslobrains.no

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 18 May '16

18 May '16

Hi Doug, Sorry- I've added entire correspondence onto the end of this e-mail. I don't think the disk filled up as I am on a 3 TB hard drive and I still have ~2 TB of free space on my disk. Anything else you think it could be? Thanks! Joseph Aloi Please remember to include previous correspondence otherwise we can't keep track of the problem! Eg, I don't have the previous email to see what the error was. Is it possible that the disk filled up? On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > Hi Doug, > > Yes, you are correct- data I have previously processed without any > problems is no longer being processed. > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > ago so I have not changed my freesurfer version recently. > > Thanks! > > Joseph Aloi > Graduate Student, MD/PhD Scholars Program > Department of Pharmacology and Experimental Neuroscience > University of Nebraska Medical Center > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > Boys Town National Research Hospital So the exact same data set is now generating an error whereas it ran smoothly before? What version of FS are you using? Did you change versions? doug On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > Hi freesurfer experts, > > I have recently begun to use freesurfer to do structural MRI > analyses. I have been able to successfully process about 40 > structural scans with recon-all thus far, but starting a few days ago, > I started getting this error whenever I run recon-all: > > WARNING: file > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > contain a Siemens ASCII header > > has this file been anonymized? > > ERROR: cannot unpack mosiacs without ASCII header > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016 > > Here are a few of the troubleshooting steps I’ve tried to track down > the cause of the error: > > -- Re-run recon-all with a couple of scans from my dataset that I have > already successfully processed > > - - Re-run recon-all the same datasets but on a different computer > > - - Re-convert the scans from .ima files to dicoms in osirix, then > run recon-all > > > For all of these steps, I have gotten the exact same error message. > The files should be anonymized, since I used osirix’s “anonymize and > convert” function to generate the dicom files (the scans were given to > me as .ima files). > > Any suggestions on what to try next? > > Thank you! > > > Joseph Aloi > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities
by Navena Rebecca Lingum 18 May '16

18 May '16

Dear FreeSurfer experts, My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command? Navena Lingum

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3T flag
by Kasper Jessen 18 May '16

18 May '16

Dear FreeSurfer group, Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment. However, where can i find the documentation for the above? Best regards, Kasper

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T2pial and [LONG]
by Kasper Jessen 18 May '16

18 May '16

Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen

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Same coordinates for all labels
by Nabin Koirala 18 May '16

18 May '16

Dear FS team, I am trying to find the centroid using mri_surfcluster using the following command but I am getting the same coordinate for all labels. I couldn't quiet understand what's wrong. Your suggestion would be really appreciated. NOTE: The coordinates differs for hemisphere. mri_surfcluster --in ./S/surf/rh.thickness --clabel ./S/centroid/rh.frontalpole.label --sum ./S/centroid/sum.rh.6.label --centroid --thmin 0 --hemi rh --subject S Thank you. Regards, Nabin

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