Freesurfer

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30084 discussions

mri_aparc2aseg doesn't write output
by Ellen Ji 23 Jul '20

23 Jul '20

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

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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
by Douglas N. Greve 23 Jul '20

23 Jul '20

Yep, I just found that error yesterday. I put a new longmc script in that same location with another fix -- but I have not fully tested it yet:) On 7/21/2020 1:12 AM, Knut J Bjuland wrote: > > External Email - Use Caution > > Thanks it worked for subjects with more than one timepoint but when I > ran on subjects with one timepoint I get this error? I can upload this > subjects. > > > mri_robust_template --mov > /cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz > /cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz --ixforms > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002.lta > --average 1 --noit --template > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz > --iscalein > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001-iscale.txt > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002-iscale.txt > > > 7.1.0 > > --mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz as > movable/source volume. > --mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz as > movable/source volume. > Total: 2 input volumes > --ixforms: Will use init XFORMS. > --average: Using method 1 for template computation. > --noit: Will output only first template (no iterations)! > --template: Using > /cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz > as template output volume. > --iscalein: Will use init intensity scales > reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz'... > converting source > '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz' to bspline ... > MRItoBSpline degree 3 > reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz'... > converting source > '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz' to bspline ... > MRItoBSpline degree 3 > error: No such file or directory > error: > ltaReadFile(/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta): > can't open file^@ > Segmentation fault (core dumped) > ERROR: > @#@FSTIME 2020:07:20:23:24:12 longmc N 5 e 17.11 S 0.79 U 1.54 P 13% > M 73600 F 111 R 30867 W 0 c 319 w 50082 I 48874 O 142592 L 42.23 41.81 > 41.92 > @#@FSLOADPOST 2020:07:20:23:24:29 longmc N 5 42.24 41.84 41.92 > Linux c5-57 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 KG01_Run1.long.KG01_Run1_base exited with ERRORS at Mon > 20 Jul 23:24:29 CEST 2020 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > #New# invocation of recon-all > > > > > > On 17/07/2020 16:28, Douglas N. Greve wrote: >> I think you might have found a bug when a cross subject has more than >> one input. Can you download >> https://gate.nmr.mgh.harvard.edu/safelinks/greve/longmc >> Copy it to $FREESURFER/bin (make a copy of the one that is there) >> Then re-run? >> thanks >> >> >> On 7/16/2020 11:57 AM, Knut J Bjuland wrote: >>> >>> External Email - Use Caution >>> >>> Thanks >>> Sure, >>> >>> Here is the log file. >>> >>> Knut Jørgen >>> >>> >>> 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: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> 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 Jørgen Bjuland >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >> >> 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. >> >

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area.pial files for fsaverage
by Xiaojiang Yang 23 Jul '20

23 Jul '20

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

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Subcortical Structure Pial Line Exclusion
by Angel Hammond 23 Jul '20

23 Jul '20

External Email - Use Caution Hello Freesurfer Experts, I think I may already know the answer to this, but just wanted to check in to be sure. I know that in general when checking the recon for a subject for pial and wm line correctness, that subcortical structure segmentation within those lines is not that important to correct. I was looking at a subject that looks to be be omitting subcortical structures from the pial line and persists for many slices. Is this something that needs to be corrected with wm edits or is this not to be worried about? I included some screenshots of the area. Thanks! Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Anatomical cluster description table from mri_glmfit-sim?
by Fred Sampedro 23 Jul '20

23 Jul '20

External Email - Use Caution Dear FS experts, From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance: Supramarginal gyrus: X vertices, X mm^2, peak T-value=X Superior frontal gyrus: Y vertices, Y mm^2, peak T-value=Y ... That is, the % of significant vertices in the statistical map belonging to each region of the default FS atlas. I know that the cache.th13.abs.sig.cluster.summary file "summarizes" each cluster by a label, but clearly large clusters are made of several different anatomical regions that I would like to report. In other words, I wonder if there's an easy way to obtain a cluster description report similar to the one provided by the xjview toolbox for voxelbased maps in MNI space. I know I could probably achieve it by scripting, i.e. but looping through each ROI extracted from an atlas in fsaverage space and applying a mask with the glmfit map and then computing the overlap and such. But probably there's an easir way, or someone has already thought about it. I tried to search about this topic in the archive but failed to find a clear solution, probably I was not searching by the appropriate words. Thanks a lot in advance,

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outlier detection and remove
by Zeng, Qi 23 Jul '20

23 Jul '20

External Email - Use Caution Hi, I have a question about how to handle outliers in aparc, aseg and tracula results? Usually, each subject has one result regarding one measurement and I detect and remove outliers using barplot. However, for results in freesurfer, we have multiple outcomes for each region in terms of measurements of aparc, aseg and tracula. Do we detect outliers for specific regions or tracts and remove the outliers? Or detect which subjects have outliers consistently for all the regions, and then we remove the subjects? Thank you so much ! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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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 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? 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? 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 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

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Motor Cortex Label/Mask
by Anja Samardzija 23 Jul '20

23 Jul '20

External Email - Use Caution Hi, I was wondering if there is a way to extract the whole motor cortex (not the separate regions of the motor cortex, but all of these regions together) of a subject following running recon-all on the subject. Thank you, Anja

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tksurfer - failed to calloc
by Nasr, Shahin,Ph.D. 22 Jul '20

22 Jul '20

Hi Surfers, I get the following error when I use tksurfer for one of our subjects: znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes! To clarify, this error is only limited to freesurfer version 6.0 and 7. But version 5.3 works fine with the same subject. Regards

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Join the final round of the IronTract Challenge
by Yendiki, Anastasia 22 Jul '20

22 Jul '20

Dear all - This is your chance to enter the final round of the IronTract Challenge. First, make sure to check out the results of round 1 of the challenge, along with other great work in the ISMRM Orientation Modelling & Fibre Tractography oral session, and join us for the Q&A: https://ww5.aievolution.com/ism2001/index.cfm?do=ev.viewEv&ev=3702 Then join us for round 2! This round requires less work by participants, as we have fixed the pre- and post-processing based on the results of round 1, and those steps will be provided. All you have to do is add your favorite orientation reconstruction and tractography method, stir, and serve chilled. Participants will have further opportunities to participate in publications that will result from the challenge. As in the previous round, the challenge is hosted on the QMENTA platform. Detailed instructions are provided here: http://irontract.mgh.harvard.edu/compete-round2/ See you at ISMRM! On behalf of the organizers, Anastasia Yendiki. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://scholar.harvard.edu/a-y

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