Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Fwd: Re: Segmentation with FreeSurfer 7.1
by Sara PONTICORVO 24 Jul '20

24 Jul '20

External Email - Use Caution Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1 Message-ID <d7c325ac-e3a9-41a6-3cf0-17c35e0b4749(a)mgh.harvard.edu> Hi, thanks a lot. What do you mean for topological default? We have checked our data, and there aren't any visible artifacts (if you were referring to this kind of things). Actually we have seen these problems in about 50% of the already acquired data. If it can be useful for you we can also send you the raw DICOM images to check yourself. It is possible that there are some default settings in the 7.1 recon-all pipeline that we can adjust? Thanks again, Sara -- Sara Ponticorvo PhD Student Departement of Medicine Surgery and Dentistry, University of Salerno

2 1

mesh referential
by TACONNE Marion (INTERN) 24 Jul '20

24 Jul '20

External Email - Use Caution Hello, I would like to know in which referential is the meshes ( lh.smoothwm for example). Is it RAS ? If not, how can we change the mesh referential in this referential. Thank you in advance for your time and answer. Best regards, Marion Taconné This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) you should not read, disclose, or copy it, (ii) please notify sender of your receipt by reply email and delete this email and all attachments, (iii) Dassault Systèmes does not accept or assume any liability or responsibility for any use of or reliance on this email. Please be informed that your personal data are processed according to our data privacy policy as described on our website. Should you have any questions related to personal data protection, please contact 3DS Data Protection Officer at 3DS.compliance-privacy(a)3ds.com<mailto:3DS.compliance-privacy@3ds.com> For other languages, go to https://www.3ds.com/terms/email-disclaimer

2 1

Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password
by fsbuild 24 Jul '20

24 Jul '20

External Email - Use Caution Hello Nuri, I am sending the password directly to your email. -R. On Jul 24, 2020, at 09:30, Choi, Nuri <nuri.choi(a)wustl.edu> wrote:        External Email - Use Caution        Hi,I followed the given instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email - may I request the password as well? Sorry if this is quite redundant on your end...Thank you very much,-Nuri_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

1 0

Extract the cerebellum
by Camargo, Aldo 24 Jul '20

24 Jul '20

External Email - Use Caution Hi Freesurfer experts, I am trying to extract only the cerebellum and then save it to nii file. How can I do it with freesurfer ? Thanks a lot and have a nice day, Aldo

2 1

FreeSurfer 7.1.0 VirtualBox Installation password
by Choi, Nuri 24 Jul '20

24 Jul '20

External Email - Use Caution Hi, I followed the given instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email - may I request the password as well? Sorry if this is quite redundant on your end... Thank you very much, -Nuri

1 0

Re: [Freesurfer] How to do permutation for multiple comparison correction?
by Xiaojiang Yang 23 Jul '20

23 Jul '20

External Email - Use Caution Hi Doug, For the first question, you answered "It is unusual, though it should work". Could you please briefly describe the way FS used to permute (based on my notation v0, v1, ... vn)? Or, the usual way to permute? The way I described seems to be the only way I can think of. Looking forward to your help here. Thanks a lot! Xiao Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 23 Jul 2020 07:37:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> On 7/21/2020 11:45 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space." By "In the ROI", I mean for all vertices listed in the label file. Here, I am talking about a test subject and n control subjects, they are all considered in the same reference subject space - fsaverage. A ROI is defined by a label file for the subject fsaverage. So, I am comparing the test subject and control group on the same ROI region, vertex by vertex. I want to permute points in the test subject and points in all subjects in control groups. I am not talking about permuting vertex locations; I am talking about permuting values (thickness in my case) from subjects on each vertex. For example, for vertex i, I have one value (v0) from test subject, and n values (v1, v2,...vn) from control subjects: test subject control subjects v0 v1, v2, ...... vn One way of permutation would be: test subject control subjects v1 v0, v2, ...... vn Is this a reasonable way to do permutation? It is unusual, though it should work. 2. "Not sure. You cannot discriminate between the groups when you are doing permutation" By doing the permutation many (say 1000) times, I want to get the probability distribution of the sampling (observed or test) data inside the ROI area, so that I can decide if I should reject or accept null hypothesis based on cluster-wise significance level. What problems do you think I have in this idea? That should work. I'm not sure what my original concern was Thanks a lot! On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how mri_glmfit-sim does the permutation. The link here http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has <http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has> a simple description for how to do permutation, but I don't quite understand the 1st step: Permute the design matrix. To me, permute the design matrix means permute the matrix rows here, but still hard to understand why permuting matrix rows does the trick. This is pretty standard in permutation. I think Tom Nichols has some basic tutorials on how permutations work. Anyway, I will not use any design matrix in my customized implementation, so it does not matter for now. My problem can be described as follows: if I have a ROI (a label file) on fsaverage, and I have a test subject and a group of control subjects whose thickness values on every vertex in this label are all known. (The test subject and control subjects are all using fsaverage reference space). I want to compare this test subject's thickness within the ROI to a control group of subjects (within the same ROI). This is a multiple-comparison problem, so I want to use permutation to get less FP rate. My question is: How do I permute the test subject's points and control subjects' points in ROI? Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space. My understanding is that: for each point in the label, I randomly re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is the number of subjects in control group). And when all points in the label are done, this is only 1 permutation. I will need at least 1000 times of permutation to get the comparison statistics. Is my understanding right? Not sure. You cannot discriminate between the groups when you are doing permutation Thank you! Xiao _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

nu_correct error
by Bahrani, Ahmed A. 23 Jul '20

23 Jul '20

External Email - Use Caution Hello Freesurfer experts, I have a question related to the singularity container to run a bash script that contains a freesurfer's commend "nu_correct". The singularity container only runs as a root user login and gives error as shown below with a general user login. ================================================================================== ---Error message--- evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running evaluate_field (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) -------------------------------------------------------------------- ---Error message--- ncvarput: ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running minccalc (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) -------------------------------------------------------------------- Would you advise, please? Thanks, Ahmed

2 4

Cortical Parcellations in FreeDurger 7
by Al Qadi, Ameen 23 Jul '20

23 Jul '20

External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: - Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROIs, but got empty ROI files. - Given that Freesurfer version 7 contains segmentations not previously generated in recon-all (i.e. hippocampal subfields), is it possible to extract these ROIs using aparc+aseg images generated using previous versions of Freesurfer? Or do we need to repeat the cortical parcellations (i.e. rerun recon-all) using FS7? I’d highly appreciate your time and feedback on this matter. Thank you. Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

2 8

Re: [Freesurfer] mri_aparc2aseg doesn't write output
by Douglas N. Greve 23 Jul '20

23 Jul '20

does the mri folder exist? do you have write permission to it? is the disk out of space? On 7/23/2020 11:04 AM, Ellen Ji wrote: > > External Email - Use Caution > > Yes, exactly, I am running it from > /home/eji/projects/spins/preproc/freesurfer/subjects/w0. > > (using a virtual machine, but ran mri_aparc2aseg a few weeks ago with > no problem) > > On 7/23/2020 4:56 PM, Douglas N. Greve wrote: >> Sorry, it should be from >> /home/eji/projects/spins/preproc/freesurfer/subjects/w0 >> (without the /mri) >> >> On 7/23/2020 8:37 AM, Ellen Ji wrote: >>> >>> External Email - Use Caution >>> >>> Dear experts, >>> >>> I am running mri_aparc2aseg and, based on the output, it seems to >>> run through successfully until the very end where it does not >>> actually write the file (I receive "error: niiWrite(): error opening >>> file mri/aparc.500+2mm.nii.gz"). However, I am 100% sure that I have >>> writing access in the directory. Below you will see the details. Do >>> you know why I am having this issue? Thank you for your time, Ellen >>> >>> mri_aparc2aseg \ >>> > --s SPN01_CMH_0001_01 \ >>> > --annot 500_sym.aparc \ >>> > --wmparc-dmax 2 \ >>> > --labelwm \ >>> > --hypo-as-wm \ >>> > --o mri/aparc.500+2mm.nii.gz >>> SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0 >>> subject SPN01_CMH_0001_01 >>> outvol mri/aparc.500+2mm.nii.gz >>> useribbon 0 >>> baseoffset 0 >>> labeling wm >>> labeling hypo-intensities as wm >>> dmaxctx 2.000000 >>> RipUnknown 0 >>> 8 avail.processors, using 1 >>> >>> Reading lh white surface >>> /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.white >>> >>> Reading lh pial surface >>> /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.pial >>> >>> Loading lh annotations from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/lh.500_sym.aparc.annot >>> reading colortable from annotation file... >>> colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) >>> Have color table for lh white annotation >>> >>> Building hash of lh white >>> >>> Building hash of lh pial >>> >>> Reading rh white surface >>> /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.white >>> >>> Reading rh pial surface >>> /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.pial >>> >>> Loading rh annotations from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/rh.500_sym.aparc.annot >>> reading colortable from annotation file... >>> colortable with 161 entries read (originally /scratch/tmpdir.annot2std.12874/seg.1.073.xhemi.ctab) >>> Have color table for rh white annotation >>> >>> Building hash of rh white >>> >>> Building hash of rh pial >>> Loading ribbon segmentation from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz >>> Loading filled from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz >>> >>> Loading aseg from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/aseg.mgz >>> ASeg Vox2RAS: ----------- >>> -1.00000 0.00000 0.00000 128.00000; >>> 0.00000 0.00000 1.00000 -128.00000; >>> 0.00000 -1.00000 0.00000 128.00000; >>> 0.00000 0.00000 0.00000 1.00000; >>> ------------------------- >>> >>> Labeling Slice (256) >>> 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 >>> 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 >>> 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 >>> 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 >>> 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 >>> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 >>> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 >>> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 >>> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 >>> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 >>> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 >>> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 >>> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 906029 >>> Used brute-force search on 0 voxels >>> Fixing Parahip LH WM >>> Found 1 clusters >>> 0 k 791.000000 >>> Fixing Parahip RH WM >>> Found 3 clusters >>> 0 k 751.000000 >>> 1 k 1.000000 >>> 2 k 2.000000 >>> Writing output aseg to mri/aparc.500+2mm.nii.gz >>> error: niiWrite(): error opening file mri/aparc.500+2mm.nii.gz >>> #VMPC# mri_aparc2aseg VmPeak 1376092 >>> mri_aparc2aseg done >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] area.pial files for fsaverage
by Xiaojiang Yang 23 Jul '20

23 Jul '20

External Email - Use Caution OK. I see that file. So that is the pial surface area for fsaverage subject. Thank you! Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 23 Jul 2020 07:54:35 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Do you not see ?lh.pial.avg.area.mgh in $FREESURFER/subjects/fsaverage/surf ? On 7/21/2020 3:11 PM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS developers, I have noticed that for each subject, there are ?h.area and ?h.area.pial files under the $SUBJECT_DIR/$subject/surf sub-directory. According to Bruce's words from here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23751.html, they are for white surfaces and pial surfaces respectively. But for the fsaverage subject, I only find file ?h.area; there are no ?h.area.pial files existing. Could you tell me why? and where can I get those files? Thanks! Xiao _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer