Freesurfer November 2020

freesurfer@nmr.mgh.harvard.edu

107 participants
149 discussions

monkey atlas D99
by Francesca Strappini 23 Dec '20

23 Dec '20

External Email - Use Caution Dear FreeSurfer experts, I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion? Thank you Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Cortical thickness volume ROI to surface {Disarmed}
by Alina Rojas 17 Dec '20

17 Dec '20

External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u… <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u…> but after mri_vol2surf I get this message, I can’t visualize the ROI on the surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina Rojas. srcvol = M1_L.nii.gz srcreg = tmp.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: using NIfTI-1 qform Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 1.00000 0.00000 0.00000 2.49380; 0.00000 0.00000 1.00000 -22.50500; 0.00000 -1.00000 0.00000 -9.53872; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75073 Writing to lh.fsaverage.M1_L.mgh Dim: 163842 1 1 surfcolor: Subscript out of range.

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question about PVC of PETSurfer
by 蒋袁芳 13 Dec '20

13 Dec '20

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough, it made the SUVr of hippocampal subfield we get is not accurate. So we want to use the PVC function of PETSurfer. Whether the PETsurfer output the result of PET image after PVC ? so that we can use it directly to registering with MRI image. If it doesn't output the result, can we save it in some ways? Thank you for your guidance.

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Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}
by Donatienne Van Weehaeghe 07 Dec '20

07 Dec '20

External Email - Use Caution Dear, We also noticed a bad segmentation in another subject in the frontal cortex (see attached figure) which was correctly done using CAT12. Can we change some parameters to fix this? Thank you Kind regards Donatienne [image: image.png] Op do 19 nov. 2020 om 14:33 schreef Donatienne Van Weehaeghe < donatiennevanweehaeghe(a)gmail.com>: > [image: HD_CAU_T1_MR.JPG] > Dear, > > In the attachment the figures.The surface placement is ok. The cautate is > smaller than the segmentation. > > Kind regards > Donatienne > > > > Op wo 11 nov. 2020 om 17:01 schreef Douglas N. Greve < > dgreve(a)mgh.harvard.edu>: > >> The caudate segmentation would not affect the surface placement. Is the >> surface placement ok? Can you send a pic of the caudate error? >> >> On 11/6/2020 9:58 AM, Donatienne Van Weehaeghe wrote: >> >> External Email - Use Caution >> Dear, >> >> Would there be another option to fix this? >> >> Kind regards >> Donatienne >> >> >> Op do 5 nov. 2020 om 17:38 schreef Donatienne Van Weehaeghe < >> donatiennevanweehaeghe(a)gmail.com>: >> >>> The subcortical structures were not delineated correctly, especially the >>> nucleus caudatus which had a lot of atrophy in this particular patient >>> group. >>> >>> Kind regards >>> Donatienne >>> >>> Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve < >>> dgreve(a)mgh.harvard.edu>: >>> >>>> I don't think CAT creates white or pial surfaces, so no. What is wrong >>>> with your FS analysis? >>>> >>>> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: >>>> >>>> External Email - Use Caution >>>> Dear, >>>> >>>> The segmentation using Freesurfer was incorrect, however we have a good >>>> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? >>>> >>>> Kind regards >>>> Donatienne >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… <https://secure-web.cisco.com/1ZxmEs2Pk3BSMewoFlR47-yhqcFOo6DC4cKshyj4rTlsuL…> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… >>>> <https://secure-web.cisco.com/1ZxmEs2Pk3BSMewoFlR47-yhqcFOo6DC4cKshyj4rTlsuL…> >>> >>> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… > >

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Extract he value of area and volume in the fsaverage for every subject
by 李梦君 07 Dec '20

07 Dec '20

External Email - Use Caution Dear FreeSurfer Developers: I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University

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Fwd: Longitudinal pipeline
by vittal korann 04 Dec '20

04 Dec '20

External Email - Use Caution Hello FS experts Thank you for your kind response. This is regarding my previous mail. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format. Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: the first is the baseline and the second one is after 3 months of yoga therapy. Wish to know how can I proceed with my available data. Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise, it will be confounded with time. Yes, I used the same across the study. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there. Looking forward to your response. Thanks, Vittal

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Re: [Freesurfer] tkregister issue with reg-feat2anat {Disarmed}
by Walsh, Erin 02 Dec '20

02 Dec '20

External Email - Use Caution Hi Dr. Greve, Our IT team replaced the reg-feat2ant file on the university HPC. When I reran a test subject, it resulted in a "command not found" error. See attached screenshot. I notified IT and they stated the following: "Since the only change made by admins was putting that new file in place, so they just put the old file back in place. You can try running the script again to see if that 'command not found' error goes away. If not, then you need to report the error back to the author that provided the file. " With the previous reg-feat2anat file, the bug I initially emailed about replicated. Do you have any suggestions for what may be causing the error? Thanks! Erin https://secure-web.cisco.com/1Xt5TzuhfYGMFSQ1E2hCKW008efsUaiJNMtBUxoHORy7dS… -- Erin Walsh, Ph.D. Assistant Professor University of North Carolina-Chapel Hill Department of Psychiatry Chapel Hill, NC 27599-3367 erin_walsh(a)med.unc.edu pronouns: she/her ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Thursday, November 12, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 201, Issue 19 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1PrXXNA2YRR-YEzLxXK-oIH4gfUWRVVoD9R3JNaZFZF8kG… 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: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (???) 2. Re: tkregister issue with reg-feat2anat {Disarmed} (Douglas N. Greve) 3. Re: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (Douglas N. Greve) 4. Re: Sulc maps (Douglas N. Greve) 5. Re: Help with MRI labels (Douglas N. Greve) 6. mris_pmake error - freadFloat: fread failed (Nasr, Shahin,Ph.D.) 7. Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed} (Park, James) 8. Re: Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed} {Disarmed} (fsbuild) 9. Re: Help with MRI labels {Disarmed} (Alberto Del Cerro Leon) ---------------------------------------------------------------------- Message: 1 Date: Thu, 12 Nov 2020 18:39:44 +0800 (GMT+08:00) From: ??? <mengjun(a)csu.edu.cn> Subject: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6071ada5.3fd7.175bc0a2c24.Coremail.mengjun(a)csu.edu.cn> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject? (2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2?Blue color). Is this correct? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005 Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-11 23:58:20 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} Sorry, try this mri_segstats --i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) On 11/5/2020 10:26 PM, ??? wrote: External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-05 22:37:07 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} Try --slabel fsaverage lh /path/to/lh.areapial.label On 11/2/2020 10:24 PM, ??? wrote: External Email - Use Caution Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) I did not get a text file including the areas of all subjects. Is this code correct? -----????----- ???:"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> ????:2020-11-02 23:36:14 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you input) all your subjects for that label. On 10/30/2020 10:37 PM, ??? wrote: External Email - Use Caution Dear Professors: I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview Then the value of the label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions: (1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values? (2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects Best wishes Mengjun Li -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-10-30 23:40:30 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology. On 10/29/2020 9:51 PM, ??? wrote: External Email - Use Caution Dear FreeSurfer Developers: I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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extracting mask for basal ganglia, deep grey, and centrum semiovale
by miracle ozzoude 02 Dec '20

02 Dec '20

External Email - Use Caution Hello Experts, I did like to create a mask for basal ganglia, deep grey matter, and centrum semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) however, how do I extract the last one. What mask should I use to extract the centrum semiovale? I don't want to include the cerebellar white matter. Thanks. Best, Paul

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Issue with custom label
by Catherine Tallman 02 Dec '20

02 Dec '20

External Email - Use Caution Hello, After running mri_vol2label I created a custom label named test.label. When I try to load the label onto lh.pial, I receive the following error: "Could not load label from <path>". The file is saved within the path folder itself. Within the terminal I receive the warning "label has not been mapped to surface". I was wondering what might be causing this issue? Attached is the label file. mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.parahippocampal. label Thank you, Catherine -- ------------------------------------------------ Catherine Tallman, M.A. Graduate Student CNS Laboratory of Memory and Brain University of California, San Diego

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Freesurfer November 2020