Freesurfer

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dat to lta
by John Anderson 17 Aug '17

17 Aug '17

Hi FS experts, Is there any way to convert the registration matrix reg.dat to reg.lta? Thank you John

3 4

mask alignment problem/mri_mask
by Yagmur Ozdemir 19 17 Aug '17

17 Aug '17

Hello freesurfer experts, A volume file I want to save as a mask(the orange/red shaded areas in the picture) on top of my volume file does not align as seen in the picture. I have used mri_vol2vol to align the mask to my native volume but apparently it did not work out. I am trying to correct this by using mri_mask now; I tried to use the option -xform %s which apparently applies the LTA transform to align mask to input volume, but now I get this error; >>lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$ mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii MW_aTAl_masked.nii transform file name is %s WARNING: hdr.dim[4] = 0 (nframes), setting to 1 niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm DoAbs = 0 Apply the given LTA xfrom to the mask volume Reading transform ... ltaReadFile(%s): can't open file No such file or directory mri_mask.bin: could not read transform file %s No such file or directory I would deeply appreciate if someone could help me sort out this mess. Thank you all! Best, Idil

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Using own parcellation atlas
by Julie Hall 17 Aug '17

17 Aug '17

Hi experts, I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions: - I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer? - Can I run this step in autorecon3 (step 28)? Or should I rerun recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)” Thank you, Julie

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-nuiterations and -norm3diters under FreeSurfer 6.0
by Antonio Algaze Beato 17 Aug '17

17 Aug '17

Hi, I have a question regarding -nuiterations and -norm3diters. I would like to get a feel for the options available for fine-tuning the intensity normalization in FreeSurfer 6.0. I've seen mention of -nuiterations on some posts. Is this still an option in FreeSurfer 6.0? The reason I ask is because under the "Expert Preferences" section of recon-all -help there's only mention of "-norm3diters". However, further down, under the second "Expert Preferences" section, there's a description of -nuiterations as well as -norm3diters. Thanks!

2 1

Skullstriping problems
by MATEUS ROZALEM ARANHA 17 Aug '17

17 Aug '17

Hi, I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using: *recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>* and than *recon-all -autorecon-pial -subjid <subject name>* But nothing changed. Do I need to run recon-all all over? Thanks, Mateus

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Re: [Freesurfer] Response to Freesurfer list email
by Bruce Fischl 17 Aug '17

17 Aug '17

Hi Rose, you should post to the list as you will get better and faster answers (although this time I know it didn't work so well for you). I believe Martin published these numbers Bruce On Thu, 17 Aug 2017, Van Der Deijl, Rosanne wrote: > Dear Bruce, > > I think my message might have gotten lost in the Freesurfer mailing list > stream, so that's why I'm sending it to you again. Thank you in advance for > your help! > > Date: Mon, 14 Aug 2017 14:08:24 +0000 > From: "Van Der Deijl, Rosanne" <RVANDERDEIJL(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] test-retest variability small subcortical > regions > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1D58C89E05A85B4E9512CDEA158803141CB99976(a)PHSX10MB5.partners.org> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, > > I mean for the longitudinal analysis. > Forgot to mention this, sorry! > > Kind regards, > > Rose > > Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Test-retest reliability small subcortical > regions > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1708111239430.24300(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Rose > > do you mean cross-sectional or longitudinal analysis? > > cheers > Bruce > > On Fri, 11 Aug 2017, > Van Der Deijl, Rosanne wrote: > > > Dear Freesurfer team, > > > > I was wondering what the test-retest reliability is of comparing small > > regions in the subcortical volume, e.g. the amygdala. Has this improved > with > > the 6.0 version? > > > > Thank you! > > > > Kind regards, > > > > Rose > > >

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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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Freesurfer