Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

AD cortical thickness signature
by Yi, Hyon-Ah 17 Aug '17

17 Aug '17

Dear FS experts I’m wondering whether there are ways of getting the single value of ROIs. I mean to get the value of cortical thickness of AD signature areas, such as supra marginal gyrus, inferior frontal cortex.. and so on .. the values of some areas can be get using aparcstats2table (in the Desikan atlas) as single value however, in the case of frontal cortex, there is no single value for it. can I get the single value from just averaging of two cortical area ? or are there another way ? Regards, Hyon-Ah

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

16 Aug '17

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

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Re: [Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis
by Douglas N Greve 16 Aug '17

16 Aug '17

posting the response to the list: The problem is that femalezero and femaletwo only have 4 and 3 subjects, respectively. As you are trying to estimate 4 slopes + an intercept, you will need at least 5 subjects per group. doug On 08/16/2017 03:27 PM, Sullivan, Danielle Renee wrote: > > Hi Doug, > > > I am just following up to this email. If you prefer I can repost on > the FreeSurfer mail archive. > > > Thanks, > > Danielle R. Sullivan (Miller), Ph.D. > > National Center for PTSD > > VA Boston Healthcare System Jamaica Plain > > Boston University School of Medicine > > OFFICE: (857) 364-4022 > > > ------------------------------------------------------------------------ > *From:* Sullivan, Danielle Renee > *Sent:* Friday, August 11, 2017 1:33:03 PM > *To:* Douglas N Greve > *Subject:* Re: [Freesurfer] Matrix ill-conditioned error for dods > thickness mri_glmfit analysis > > I am still getting the same error. My apologies for the back and forth. > > > Here are updated files (now there are 5 classes and contrast mtx has > been changed to reflect that). > > > Danielle R. Sullivan (Miller), Ph.D. > > National Center for PTSD > > VA Boston Healthcare System Jamaica Plain > > Boston University School of Medicine > > OFFICE: (857) 364-4022 > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *Sent:* Friday, August 11, 2017 1:10:53 PM > *To:* Sullivan, Danielle Renee > *Subject:* Re: [Freesurfer] Matrix ill-conditioned error for dods > thickness mri_glmfit analysis > remove the definition too > > > On 08/11/2017 12:46 PM, Sullivan, Danielle Renee wrote: > > > > Hi, > > > > > > Thank you for the tips. I tried doing both and still run into the > > error (although now I get a warning that the class femaleone is > > defined but not used). Attached is my new FSGD (now all variables > > normalized via a Z-score), XG.mtx, Contrast, and Terminal output. > > > > > > Thanks again for the help! > > > > > > Danielle R. Sullivan (Miller), Ph.D. > > > > National Center for PTSD > > > > VA Boston Healthcare System Jamaica Plain > > > > Boston University School of Medicine > > > > OFFICE: (857) 364-4022 > > > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > > *Sent:* Friday, August 11, 2017 11:12:21 AM > > *To:* Sullivan, Danielle Renee > > *Subject:* Re: [Freesurfer] Matrix ill-conditioned error for dods > > thickness mri_glmfit analysis > > there appear to be two problems. One is that you only have one instance > > of femaleone. This might be ok if you had no covariates, but you can't > > estimate a covariate slope from one data point. Second, the scale of > > your covariates is much different, so you may need to normalize them. I > > would try removing the lone femaleone and rerun > > > > > > On 08/11/2017 10:35 AM, Sullivan, Danielle Renee wrote: > > > > > > Hi Doug, > > > > > > > > > Thanks for your response and help. > > > > > > > > > Attached is the matrix and the terminal output. Please let me know if > > > you need anything else. > > > > > > > > > > > > Danielle R. Sullivan (Miller), Ph.D. > > > > > > National Center for PTSD > > > > > > VA Boston Healthcare System Jamaica Plain > > > > > > Boston University School of Medicine > > > > > > OFFICE: (857) 364-4022 > > > > > > > > > can you send the design matrix Xg.mtx and the full terminal output? > > > On 08/08/2017 09:13 AM, Sullivan, Danielle Renee wrote: > > > > > > > > Hi FreeSurfer Experts, > > > > > > > > > > > > I am trying to run a dods cortical thickness analysis examining the > > > > interaction of group on a continuous variable while controlling for > > > > other variables. > > > > > > > > > > > > Specifically, I have 6 classes (gender by three groups [zero, one, > > > > two]). I am interested in the group interaction with a continuous > > > > variable while controlling for gender (among 4 other continuous > > > > variables). I set up my fsgd file (see attached) and contrast file > > (36 > > > > dimensions- F test): > > > > > > > > *0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -1 > > 0 1 > > > > -1 0]/2* > > > > > > > > *0 0 0 0 0 0 **0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -0 > > > > -1 1 0 -1]/2* > > > > > > > > > > > > and ran this command: > > > > > > > > > > > > *mri_glmfit --y > > > > > > > **lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh > > > > > > > > --fsgd > > > > > > > fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt > > > > > > > > dods --C > > > > > > /GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx > > > > --surf fsaverage lh --cortex --glmdir > > > > > > > lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir > > > > > > > > * > > > > > > > > > > > > But keep getting this error: > > > > > > > > > > > > *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* > > > > > > > > *--------------------------------* > > > > > > > > *Possible problem with experimental design:* > > > > > > > > *Check for duplicate entries and/or lack of range of* > > > > > > > > *continuous variables within a class.* > > > > > > > > *If you seek help with this problem, make sure to send:* > > > > > > > > * 1. Your command line:* > > > > > > > > * mri_glmfit --y > > > > > > > lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh > > > > > > > > --fsgd > > > > > > > fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt > > > > > > > > dods --C > > > > > > > /Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx > > > > > > > > --surf fsaverage lh --cortex --glmdir > > > > > > > lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir > > > > > > > > * > > > > > > > > * 2. The FSGD file (if using one)* > > > > > > > > * 3. And the design matrix above* > > > > > > > > > > > > > > > > Any idea on what I am doing wrong? > > > > > > > > > > > > Danielle R. Miller, Ph.D. > > > > > > > > National Center for PTSD > > > > > > > > VA Boston Healthcare System Jamaica Plain > > > > > > > > Boston University School of Medicine > > > > > > > > OFFICE: (857) 364-4022 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > gr...(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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > 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. > > > > > > > > > > -- > > 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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > 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/ > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Segmentation of WM hypointensities
by Rockers, Elijah D. 16 Aug '17

16 Aug '17

Hello, The Freesurfer segmentation for hypointensities is very good, but misses on some subjects, i.e. it does not include large chunks of hypointense regions in some subjects. It does fantastic picking up the periventricular hypointensities, but appears to fail on some deep WM regions. I just stumbled on an archived message that mentioned an unreleased tool that can use other contrasts to improve segmentation. Is the tool close to being available, by any chance? Or any suggestions for improving our segmentations for these? Many thanks, - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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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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Freesurfer August 2017