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Help with hippocampal subfield alignment
by Elizabeth Hall 16 Aug '17

16 Aug '17

Hello FreeSurfer Developers, I have run the hippocampal-subfields-T1 tag on a MP2RAGE scan for one of my subjects and find that the subfield segmentation for the left hemisphere only is off (pictures attached). No errors were reported in the log. Is there a way to manually reset the alignment for only one hemisphere? Or is there a reason why it might be failing to segment that hemisphere? Thank you, Elizabeth -- Elizabeth Hall ehall1027(a)gmail.com| +1 559 824 6695

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binarize white matter mask
by Elizabeth Dao 16 Aug '17

16 Aug '17

Dear experts, I need a binarized wm mask for my analysis. The wm.mgz volume includes subcortical structures so I would like to use the aseg.mgz volume. I was hoping someone could give me instructions (command-line) on how to binarize aseg.mgz so that the wm=1 and everything else is 0. Thank you in advance for your help! Liz

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Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm
by Antonin Skoch 16 Aug '17

16 Aug '17

Dear Clemens, I now see where is the problem: The current implementation of recon-all -talairach step is quite complicated, as far as I understand: The -talairach registration step produces talairach.auto.xfm. If the talairach.xfm exists, it is not overwritten by talairach.auto.xfm (unless -clean-tal is specified on the command line). For further recon-all processing steps the talairach.xfm is used. It assures that when talairach.xfm is edited (for example by tkregister2), the edits are not overwritten, but only IN THIS VERY STEP. Further step is talairach failure detection, which uses talariach.xfm. When the failure detection passes, everything is ok and recon-all proceeds further (using talairach.xfm). However, when the failure detection indicates failure, the current implementation is to use alternative talairach registration procedures - first it is trying to align to 3T-based atlas and if it also fails, it is trying to use MINC mritotal tool. And here comes the problem: In both these steps the talairach.xfm is by default OVERWRITTEN by talairach.auto.xfm. This has consequence, that when user is modyfying talairach.xfm (i.e. by tkregister2) and this modified talairach.xfm also do not pass failure detection, it is OVERWRITTEN as indicates following lines in your recon-all.log code: cp transforms/talairach.auto.xfm transforms/talairach.xfm I personally think that this is not very optimal behaviour and it deserves modification of the recon-all code by developers. So the remedy for your case would be: either try to align better your data in tkregister2, and rerun trecon-all -s subj_id -all until you pass talairach failure detection of your customized talairach.xfm. If the talairach check failed and your talairach.xfm is overwritten, you will find it in the subdirectory transforms-bak. or after tkregister2, rerun your data by adding -notal-check to your recon-all: recon-all -s subj_id -all -notal-check Antonin Dear Antonin Yes, that is the directory where - after failed recon-all - I opened, manually registered, then saved the talairach.xfm file. Before I re-ran recon-all, I reopened the modified talairach.xfm file with tkregister2 to verify that it was my manual registration, which was true. I attached the recon-all log and error files and the talairach and talairach-avi log file. Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Clemens -----freesurfer-bounces(a)nmr.mgh.harvard.edu schrieb: ----- An: freesurfer(a)nmr.mgh.harvard.edu Von: Antonin Skoch Gesendet von: freesurfer-bounces(a)nmr.mgh.harvard.edu Datum: 16.08.2017 12:23 Betreff: Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm Dear Clemens, I am almost out of ideas, since the behaviour is contrary to my expectations. I would expect that if you run your recon by recon-all -s subject_id -all the files you named before_recon-all_talairach.xfm and after_recon-all_alairach.xfm should be identical. Could you assure that after tkregister2, you saved the transform file under name talairach.xfm and put into directory /Volumes/PromisePegasus/HippocampusPreparedT1Data/subjects/x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient/mri/transforms ? What freeSurfer version are you using? Could you post full recon-all output? Antonin Hi Antonin Thank you for your reply.Here is what I did: 1. tkregister2 --mgz --s x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient --fstal 2. manual registration (see attached file “before_recon-all_talairach.xfm”) 3. re-run recon-all, which is: recon-all -s x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient -all -hippocampal-subfields-T1 This resulted in the following error message: #@# Talairach Failure Detection Wed Aug 16 08:53:15 CEST 2017 /Volumes/PromisePegasus/HippocampusPreparedT1Data/subjects/x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0622, pval=0.0034 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach \nERROR: Talairach failed!\n The file that I now find in the “transforms” folder is attached (“after_recon-all_talairach.xfm”). I also attached the two talairach.auto.xfm but I didn’t modify these at any point. (Should I? If so, how do I?) Clemens -----freesurfer-boun...(a)nmr.mgh.harvard.edu schrieb: ----- An: freesurfer(a)nmr.mgh.harvard.edu Von: Antonin Skoch Gesendet von: freesurfer-boun...(a)nmr.mgh.harvard.edu Datum: 15.08.2017 16:46 Betreff: Re: [Freesurfer] use manually defined talairach.xfm Dear Clemens, this is very strange, since the talairach.xfm is not by default overwritten in recon-all (unless you specified -clean-tal to recon-all). When you rerun your recon-all after modifying talairach.xfm, your automatic talairach registration will be saved into talairach.auto.xfm, therefore talairach.auto.xfm and talairach.xfm will be different (without editing they will be identical). See the excerpt of the recon-all -help: Talairach (-<no>talairach) This computes the affine transform from the orig volume to the MNI305 atlas using Avi Snyders 4dfp suite of image registration tools, through a FreeSurfer script called talairach_avi. Several of the downstream programs use talairach coordinates as seed points. You can/should check how good the talairach registration is using "tkregister2 --s subjid --fstal-avi". You must have an "fsaverage" subject in your SUBJECTS_DIR. tkregister2 allows you to compare the orig volume against the talairach volume resampled into the orig space. If you modify the registration, it will change the talairach.xfm file. Your edits will be *not* be overwritten unless you run recon-all specifying -clean-tal. Run "tkregister2 --help" for more information. Creates the files mri/transform/talairach.auto.xfm and talairach.xfm. The flag -tal-check will check the registration against known-good transforms. Adding the flag -use-mritotal after -talairach will use the MINC program mritotal (see Collins, et al., 1994) to perform the transform. Can you check that your edited talairach.xfm is indeed modified to default after recon-all rerun? Do the talairach.xfm and talairach.auto.xfm differ? Antonin Hi I got a Talairach Failure Detection Error and therefore did manual registration using tkregister2 following the advice at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeviewAgain following the advice on the site, I re-ran recon-all just to run into the identical error. When I checked talairach.xfm it was the same as BEFORE I did manual registration in tkregister2. The above site states: Because the talairach transformation affects everything in the stream it is necessary to rerun the whole process using your new talairach, which is a default. However, it seems this is not the default since recon-all comes up with its own talairach.xfm and overwrites my manual version, after which recon-all fails. How can I make recon-all use my manual registration?

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Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm
by Antonin Skoch 16 Aug '17

16 Aug '17

Dear Clemens, I am almost out of ideas, since the behaviour is contrary to my expectations. I would expect that if you run your recon by recon-all -s subject_id -all the files you named before_recon-all_talairach.xfm and after_recon-all_alairach.xfm should be identical. Could you assure that after tkregister2, you saved the transform file under name talairach.xfm and put into directory /Volumes/PromisePegasus/HippocampusPreparedT1Data/subjects/x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient/mri/transforms ? What freeSurfer version are you using? Could you post full recon-all output? Antonin

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T1 motion and average
by John Anderson 15 Aug '17

15 Aug '17

Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the same participant. These T1 images were acquired at the same scanning session. I have two question: 1. Is there any tool in free surfer to average these images. 2. Is the average the images a good idea to reduce noise and improve SNR 3. Do you suggest me any solution that can help to reconstruct these noisy images. Thank you for any suggestion John

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error in recon-all
by 王康程 15 Aug '17

15 Aug '17

Hello FreeSurfer Developers, I'm attempting to do recon-all for a subject. But it reported error although I try several times. The files for recon-all log and error are attached. CORRECTING DEFECT 1 (vertices=10662, convex hull=4463) normal vector of length zero at vertex 137885 with 0 faces vertex 137885 has 0 face No such file or directory Linux compute-0-106 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CTRL_011 exited with ERRORS at Tue Aug 15 04:28:55 EDT 2017 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? -- ------- Kangcheng Wang PhD, Faculty of Psychology, Southwest University, China / Visiting Research Scholor, Massachusetts General Hospital

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Re: [Freesurfer] Help with hippocampal subfield alignment
by Antonin Skoch 15 Aug '17

15 Aug '17

Dear Elizabeth, I would guess that something went seriously wrong in the recon-all with your data. Does Talairach registration and skull strip look reasonable? Antonin Skoch

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Fwd: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} {Disarmed}
by Douglas Greve 15 Aug '17

15 Aug '17

FYI -------- Forwarded Message -------- Subject: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} Date: Tue, 15 Aug 2017 09:44:19 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *Call for Nominations - OHBM Student and Postdoc Special Interest Group * Dear OHBM Members, The OHBM Student and Postdoc Special Interest Group (SIG) are seeking nominations for our 2017-2018 committee. The SIG provides a community of shared interests for OHBM trainees. The committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the annual meeting. Committee members benefit from being an integral part of the SIG, directing its activities, and working with the OHBM Executive and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. *Eligibility * * Nominees must be current students or postdocs. Students are defined as those working full time towards a graduate degree - M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of next annual meeting. * Nominees must be members of OHBM in good standing at the time of the next annual meeting * Nominees must be planning to attend the next two annual meetings in Seoul 2018 and Rome 2019 (and likely to attend the meeting in 2020). To nominate yourself for a position on the committee please fill out the nomination form and attach your CV:https://goo.gl/forms/iUF7wnMDhbdldGCG2 <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Email ohbmtrainees(a)gmail.com <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> if you have any questions. *Nominations close on the 16th September 2017. * Kind regards, OHBM Student and Postdoc SIG *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3518&conta…>

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(no subject)
by Silvia Obertino 15 Aug '17

15 Aug '17

Hello, I try to map the surface to the native space, using the following command adjusted for my data: mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname the output is: ERROR: --tval-xyz flag needs 1 argument FYI: --tval-xyz now requires a volume. So in the web-page ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat) the comand is not correct. What kind of volume can I put, to get the surface in the native space? Thank, Silvia

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SPC in surface area
by Maria A Infante 15 Aug '17

15 Aug '17

Hi everyone, I have a questions concerning the SPC values for an individual brain region. I am looking at group differences (3 groups) in SPC in surface and found one region that was significant after correcting for multiple comparisons. I want to follow up with pairwise comparisons. Is there a way to extract the SPC values for that particular region? Are these the same values as the ones on the stack file? Thanks, Alejandra

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