Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

mri_glmfit error: MatrixMultiplyD(): m2 is null
by 정현우 10 Mar '22

10 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as described on the Surface Based Group Analysis tutorial ( https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3r… I ran the following command: mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save Then I got the following error: gdfRead(): reading three_group_comparison.area.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 eTIV 1.53351e+06 139455 Class Size and Means of each Continuous Variable 1 0 42 1566070.5417 2 1 34 1515147.1360 3 2 15 1483959.5000 INFO: gd2mtx_method is dods Reading source surface /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.2.0 cwd /media/sjkim/hd2/subject_data/glm cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save sysname Linux hostname sjkim-System-Product-Name machine x86_64 user sjkim FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh logyflag 0 usedti 0 FSGD three_group_comparison.area.fsgd labelmask /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label maskinv 0 glmdir three_group_comparison.area.lh.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory three_group_comparison.area.lh.glmdir Loading y from /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 833.575 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149953 voxels in mask Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.059149 DOF = 85 Starting fit and test Fit completed in 0.0373833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140 Writing results three_group_comparison.area maxvox sig=3.0263 F=7.57212 at index 107440 0 0 seed=1645215319 error: No such file or directory error: MatrixMultiplyD(): m2 is null break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596 I used FreeSurfer version 7.2.0 and Ubuntu 20.04. I've searched the mail archives and similar errors have been reported in qdec, but I could not find any specific solution for this problem. Do you have any suggestions to solve this problem? Thank you in advance, Hyunwoo Jeong

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Re: [Freesurfer] recon-all permissions problems
by fsbuild 09 Mar '22

09 Mar '22

External Email - Use Caution Hello Giuseppe, Try the same command (with lowercase w) or use a+w and then enter your password, $ sudo chmod -R  a+w  $SUBJECTS_DIRPassword: … then test to see if it works to create a file there, i.e., it should not report permission denied ... $ touch $SUBJECTS_DIR/foo … then see if you can remove the file … $  rm  $SUBJECTS_DIR/foo If that works you should be OK. - R. On Mar 6, 2022, at 11:46, giuseppe messina <giusmex(a)gmail.com> wrote:        External Email - Use Caution        hi i am a neurosurgeon, and i am a newbie in freesurfer, nut i thin i installed it appropriately and the licence txt file is oki have a macbookpro 16 last generation with 32 gb of memorymy freesurfer version is 7.2.0the problem is that when i run recon-all ( in correct syntax) , permission issues appear; it seems that i dont have permissions to go ahead with the freesurfer.i also used ( as indicated in one of your tutorial ) the sudo chmod -R a+W $SUBJECTS_DIR command, but if i do so, a password is requested in the terminal.really, i dont know hot to solve this problem, please help me GiuseppeThank you again-- Giuseppe MessinaDept NeurosurgeryIstituto Nazionale Neurologico "Carlo Besta", MilanE-mail  giusmex@gmail.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Oracle VM - SSH
by fsbuild 09 Mar '22

09 Mar '22

External Email - Use Caution Hello Zoe, The VM is not setup out of the box with an IP address you can use to remotely login to from an outside machine.  It uses (or piggy-backs off) the existing network connection from the host machine.   This enables the VM to boot w/o needing to negotiate for a non-local IP address and it is also for security.  We don't know the policy for someone connecting a new (virtual or real physical) machine to the network the host machine is already using.  If you can remotely VNC into your host machine and see/use the desktop, then you can use the VM running on the desktop as just another application. There’s information available online about how setup a VirtualBox VM to be accessible from the outside, e.g., via ssh.   If you have IT support, you could ask them for help.  But it’s not really practical for us to support users configuring a machine to run on their local network. On Mar 9, 2022, at 14:44, Zoe O'Brien-Moran <zobrienmoran(a)cubresa.com> wrote:        External Email - Use Caution        Hello FS expertsI'm using freesurfer with the oracle VM and I need to SSH in from my host machine, I see that openSSH is installed on the VM, but haven't been able to get in. Does anyone have experience with/ advice for this?Thanks in advance Zoë_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Oracle VM - SSH
by Zoe O'Brien-Moran 09 Mar '22

09 Mar '22

External Email - Use Caution Hello FS experts I'm using freesurfer with the oracle VM and I need to SSH in from my host machine, I see that openSSH is installed on the VM, but haven't been able to get in. Does anyone have experience with/ advice for this? Thanks in advance Zoë

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Cutting the Full Surface
by Francesca Strappini 09 Mar '22

09 Mar '22

External Email - Use Caution Dear FreeSurfer experts, I'm trying to cut and flatten the full surface. I understand that tksurfer is deprecated and on my PC does not work properly. Is there an alternative way to perform the cuts? Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strappini(a)uniroma1.it <francescastrappini.stud(a)uniroma1.it>

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Using T1 FLAWS in recon-all
by Mathilde Pichon 09 Mar '22

09 Mar '22

External Email - Use Caution Hello, I know T1 MPRAGE is the prefered format to perform a recon-all segmentation. But some of my patients' data only have FLAWS images and no MPRAGE images. So is it possible to perform a recon-all with FLAWS images ? Regards, Mathilde

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ERROR: Flag -sveres unrecognized
by CALLACHAND Muntasir 09 Mar '22

09 Mar '22

External Email - Use Caution Hi, I have a problem when i try to run the function selxavg-sess<https://secure-web.cisco.com/1snqhzGaC-QpszU2KOda0ORr2TBaYIxDby42s9Iwaqfwu6…> with the optional arguments -sveres. This message occur : ERROR: Flag -sveres unrecognized Do you know what i can do to fix this? Best, Muntasir CALLACHAND

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bbregister dependencies recon-all
by Guillem París 09 Mar '22

09 Mar '22

External Email - Use Caution Hello, I'm trying to run a Boundary-based registration by using bbregister. In the documentation, it is specified that the anatomical image has to be previously analysed in FreeSurfer. I assume that means to run the "recon-all" pipeline. Now, are all the stages of "recon-all -all" needed to perform this registration? Since I am time-constrained, I would like to run as few stages as possible, so I can use bbregister. If it matters, I'm trying to register a DWI to the same subject's T1-w. Thank you! Guillem

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Error: inputs cannot have multiple frames
by HYE JUNG YOUN 09 Mar '22

09 Mar '22

External Email - Use Caution Dear Freesurfer developers, I realised some of my recon-alls been processed with the following error: ERROR: input(s) cannot have multiple frames! /Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames (I have attached the recon-all.log) I checked the mri info and I think the problem is the dimensions which is 256 x 256 x 211 x 2. I'll attach the original commands I used with mri info in txt file in case it would help you to see where I went wrong. If anyone has been through this problem or if you know what I can do to fix this, please let me know. Best, H

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Re: [Freesurfer] GLM analysis - volume and surface area
by Laura Willers de Souza 09 Mar '22

09 Mar '22

External Email - Use Caution Sorry about that! I'm resending with previous emails. The first message below is the one you didn't know how to respond to because you didn't have the previous e-mails. --------------------------------------------------------------------------------------- On 2/22/2022 9:15 AM, Laura Willers de Souza wrote: Thanks so much for the explanation! There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons. ------------------------------------------------------------------------------ On 2/21/2022 15:20 PM, Douglas N. Greve wrote: Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring truncated tetrahedra. When you run mris_preproc, it will apply a jacobian correction (like VBM). Otherwise, it operates the same as if you had a thickness value at the vertex, ie, same GLM, etc. Make sure to use permutation for correction of multiple comparisons. ----------------------------------------------------------------------------------------- On 2/21/2022 12:13 PM, Laura Willers de Souza wrote: Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!? I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me? Thanks in advance! Best, Laura.

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Freesurfer March 2022