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Many thanks for the reply,
Yep, unfortunately MG values are always much higher than SGTM ones (in all the ROIs). I wonder whether this might be related (for MG and MZ) to the absence of a normalization using the pons as a reference.
Indeed, when I look at the file with mean values extracted for each modality, I see that the pons has always 1000 as mean uptake value for no PVC and SGTM, while for MG and MZ values in the pons range from -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
Below are the commands I’ve used to obtain the MG and MZ values: 1) With Muller-Gartner (MG): mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output Then: mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum MG_ROI.txt 2) With Meltzer (MZ): mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o gtm_MZ.output Then: mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt
Do you recognize any errors in the commands?
Many thanks,
Pilar
Message: 13 Date: Thu, 16 Jul 2020 10:19:32 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] PETSurfer analysis question To: <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edumailto:d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"
The NoPVC and SGTM values are reasonable. The MG value is pretty crazy. I don't put stock in MZ. Is the MG value much higher than SGTM in other ROIs? What is your mri_gtmpvc command?
On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
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Hi Freesurfer experts,
I?ve run a PETSurfer analysis in order to compare mean?uptake values of ROIs obtained with different methods: No PVC, SGTM, MG and MZ. However, I?ve now extracted the mean values and they are extremely heterogeneous. As an example, the same ROI (lh banks of the superior temporal sulcus) has the following uptake values:
No PVC= 1.709 SGTM= 2.495 MG= 23.847 MZ= 15.564
I?m particularly worried for the huge difference between noPVC - SGTM values and MG-MZ values.
Any advice? I wonder whether this finding is normal or there is something I?ve missed.
Many thanks,
Pilar
Il giorno 15 lug 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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Today's Topics:
??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run ?????for some subjects (Douglas N. Greve) ??2. Re: mri_fieldsign error (Douglas N. Greve) ??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)
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Message: 1 Date: Wed, 15 Jul 2020 11:12:21 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects To: freesurfer@nmr.mgh.harvard.edu Message-ID: beb084b0-fe6b-c8a2-c0a5-e8bcc92769b6@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Can you send the recon-all.log file for some of the failures?
On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:
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Dear list,
As described by others on this list, recon-all with Freesurfer 7.1 on a Mac operating system seems to fail for around 10% of the subjects.
The following solution was offered:
sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... ?-o rca-long-tp-init sudo chmod +x rca-long-tp-init However, this did not solve the problem for me.
I re-ran recon-all for the same subjects, but it still failed, some of them at the following step:
"####################################### GCADIR /Applications/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs #######################################"
It simply stopped running there.
Others did finish running, but instead got a segmentation fault error.
What could I do? I have Mac High Sierra.
Annelies
Annelies van't Westeinde?| PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskav?gen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.se http://ki.se/en/startpage ______________________________________ Karolinska Institutet ? a medical university
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Message: 2 Date: Wed, 15 Jul 2020 11:14:53 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] mri_fieldsign error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5364c956-1d58-e69d-5635-6fde5dd41c91@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
I don't know what is going wrong here. One simple thing to check is to make sure that all the input files have the same number of vertices as the surface. If that is the case, then upload the subject and input files using the instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 7/15/2020 11:07 AM, Xiaomin Yue wrote:
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Hi All,
Just in case the below poster was missed.
Thanks,
Xiaomin
*From: *Xiaomin Yue mailto:yuexm@hotmail.com *Sent: *Saturday, July 11, 2020 1:43 PM *To: *Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] mri_fieldsign error
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Hi Doug,
I used FS 7.1 under WSL to analyze retinotopy data.? Since the ring and wedge were presented at a different frequency, the data had to be analyzed separately for each condition.? To get the field sign, I had to use the mri_fieldsign function to combine polar and eccen data. However, an error happened with running mri_fieldsign: ?Segmentation fault????? (core dumped)?.? The following is the command-line output.
Thanks for your help!
Xiaomin
cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO --hemi rh --sphere
sysname? Linux
hostname DESKTOP-SVDQE4Q
machine? x86_64
user???? xiaominyue
eccen real ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch???? (null)
subject???? LOO
hemi??????? rh
fwhm??????? -1.000000
nsmooth???? -1
fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew????? 1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
??? 0???? 0 45452?? 0.03? 33.2224
1018? 1000 39160? 21.33? -18.3959
2055? 2000 44734? 43.26? 33.0783
3148? 3000 49793? 65.38? 0.653687
4344? 4000 38626? 88.16? 16.7555
5529? 5000 54149 110.12? -4.90118
6706? 6000 61599 133.36? -5.74607
7971? 7000 50134 155.88? -17.5589
9165? 8000 34182 178.05? -18.9387
10591? 9000 59682 200.70? -4.60514
12034 10000 63856 223.18? -4.4884
13297 11000 41007 245.62? 27.3489
14938 12000 27365 267.70? -1.40077
16684 13000 23615 289.10? -0.518007
18048 14000 47088 309.37? 18.7017
19798 15000 21060 330.11? 15.9458
21681 16000 33067 350.27? -11.1953
23173 17000 28744 371.48? -6.18747
25112 18000 27738 392.41? -6.93845
26953 19000 20538 414.47? 2.99349
28903 20000 80583 435.98? -0.338512
30319 21000 16251 459.83? -45.2313
32174 22000 17139 483.36? -2.31642
34093 23000 13307 507.02? 19.1461
36170 24000 17826 530.65? -10.7575
37683 25000 69324 555.78? -6.17011
39666 26000 14043 583.29? -10.5151
41746 27000 76017 609.92? -0.0112556
43986 28000 84646 636.28? 1.24722
46088 29000 9763 664.26? 12.7035
48326 30000 92161 694.30? 2.03416
50431 31000 99884 724.91? 1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault????? (core dumped) mri_fieldsign --fs $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s $subjname --hemi $hemi --sphere
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Message: 3 Date: Wed, 15 Jul 2020 15:39:08 +0000 From: "O'Dell, Ryan" ryan.odell@yale.edu Subject: [Freesurfer] Extracting PET Binding Values from Inflated Surface To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BN8PR08MB5825811A87A2758B0DDC2D25F57E0@BN8PR08MB5825.namprd08.prod.outlook.com
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Hi Doug,
I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the cortical ribbon), and then displayed on the inflated hemisphere surfaces.
We would like to extract the average binding values from the cortical surface ROIs using the Desikan-Killiany atlas, but are unsure how to go about this. Is there a simple way to use aparcstats2table or a similar command to extract average values from surface ROIs as defined by the ?h.aparc.annot file?
Thanks!
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Message: 14 Date: Thu, 16 Jul 2020 17:57:28 +0200 From: Knut J Bjuland <knutjorgen@outlook.commailto:knutjorgen@outlook.com> Subject: Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Message-ID: <DB6PR05MB3494D92A68AF36388DFFCF6EC37F0@DB6PR05MB3494.eurprd05.prod.outlook.commailto:DB6PR05MB3494D92A68AF36388DFFCF6EC37F0@DB6PR05MB3494.eurprd05.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
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Thanks Sure,
Here is the log file.
Knut J?rgen
On 16/07/2020 16:12, Douglas N. Greve wrote: Can you send the log file?
On 7/15/2020 1:51 PM, Knut J Bjuland wrote:
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Dear freesurfer experts
I was able to run the same subects on the longitudinal stream using FS 6 , but when I use FS7.1 I got this error
RROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! ERROR: @#@FSTIME ?2020:07:15:18:43:31 longmc N 5 e 1.75 S 0.47 U 0.15 P 35% M 2444 F 88 R 26962 W 0 c 321 w 33906 I 19328 O 14 L 31.52 31.63 31.62 @#@FSLOADPOST 2020:07:15:18:43:33 longmc N 5 31.55 31.64 31.63 Linux c5-31 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 007_Run1.long.007_Run1_base exited with ERRORS at Wed Jul 15 18:43:33 CEST 2020
Knut J?rgen Bjuland
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