Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Running v7 with recon-all v6 files
by Alexandra Brouillard 23 Sep '22

23 Sep '22

External Email - Use Caution Hi I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ‘permission denied’ error when typing ‘$FREESURFER_HOME’ (but have the permissions/sudo). I also can’t open Freeview: by double clicking on the app, the GUI crashes, or by typing ‘freeview’ in the terminal I get a PETSC error. According to some previous forum threads, I’m thinking of downloading the v7 but would like to validate that it’s OK when using recon-all v6 files. Thank you for your support, Alexandra

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Re: [Freesurfer] FSFAST first level covariates
by Emily Iannazzi 23 Sep '22

23 Sep '22

External Email - Use Caution Hi Doug, Just following up on this to see whether there’s a way to test for both self-relevance and valence of stimuli separately from each other as well as their interaction within the same paradigm file. Our current setup is as follows: 1 – SelfRelevant (=1, included only for trials rated as “self-relevant”) 2 – ValenceOffset (=1, included only for trials rated as “self-relevant”) 3 – ValenceSlope (=valence rating) 4 – SelfIrrelevant (=1, included only for trials rated as “self-IRrelevant”) 5 – ValenceOffset (=1, included only for trials rated as “self-IRrelevant”) 6 – ValenceSlope (=valence rating) 0 – Other 0 – Case 0 – Fixation We first had 7 for “Other” and “Case” conditions but ran into a “design is ill-conditioned” error which we thought might be due to how many conditions we had coded. We’re still getting the same error with the current design and are receiving it after our “XCond=” line, which is being calculated to be 5.45e16. Do you have any insight on the best way to set this up within Freesurfer? Essentially, we want to test the equation [y = selfrelevance + valence + selfrelevance*valence], where [selfrelevance] is a binary 1/0 variable and [valence] ranges from -4 to 4, and both are individualized ratings for each word presented in the scanner. At the end, we want to be able to test the effect of selfrelevance alone, valence alone, and their interaction. Thanks for all your help on this, it is much appreciated! 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> Date: Wednesday, August 31, 2022 at 9:22 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 223, Issue 1 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/16sxEiU6wNvb3APhDY30iCD5GDB2tygSk9fz16LcJ-8vwM…<https://secure-web.cisco.com/1qcT0vI2O-CEm7vL5s0AmTXieqgysu66ANTok-YJfFa1OJ…> 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: FSFAST first level covariates (Angela Fang) 2. Bus error using VM (#@# Nu Intensity Correction) (daedalus39(a)aol.com) 3. Re: Bus error using VM (#@# Nu Intensity Correction) (fsbuild) 4. Re: sclimbic sometimes does not detect left basal forebrain (Douglas N. Greve) 5. Re: FSFAST first level covariates (Douglas N. Greve) 6. Re: FSFAST first level covariates (Angela Fang) 7. Re: Thalamic nuclei exited with ERRORS (Yann Quid?) 8. Re: Thalamic nuclei exited with ERRORS (fsbuild) 9. Re: Unable to run trac-all -prep : cannot file bvals bvecs file (Ashwati Vipin (Dr)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 31 Aug 2022 16:39:37 +0000 From: Angela Fang <angfang(a)uw.edu> Subject: Re: [Freesurfer] FSFAST first level covariates To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2A2F422F-279C-4736-885A-C609F488C21E(a)uw.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution That makes sense! And if we wanted to identify brain regions associated with valence (across self/non-self) that is unique from condition 2, can we add a 5th condition? Maybe we can code self as 2 and non-self as 1 so that condition 2 (self*valence) would be different from condition 5 (valence ratings only)? Incredibly helpful, Doug- thank you so much! From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, August 30, 2022 at 7:38 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates Oh, I think I see now. In realty, each trial is either self or not self and then you have a separate valence measure, so your coding should be 1. Self-offset 2. SelfValence 3. NoSelf-offset 4. NoSelfValence Where 1+2 are used for a self event and 3+4 are used for a noself event. If you want to test for the difference between self and noself valence slope, then you would just use -a 2 -c 4 On 8/29/2022 12:08 PM, Angela Fang wrote: External Email - Use Caution Great, thanks so much Doug- this setup makes sense to me. However, isn?t it a problem that the brain regions associated with the contrast for -a 3 and the contrast for -a 4 would be the same for trials that subjects rate as 1 (self-relevant) vs 0 (not self-relevant)? Could we code it as 2 (self-relevant) and 1 (not self-relevant)? Many thanks!! From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, August 28, 2022 at 1:07 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates I was under the impression that Self and Valence were ratings from the same event (in that mail archive, they were different events and so needed different offsets). If Self and Valence are from the same event, then you would have something like 1. Offset 2. Self 3. Valence 4. Self*Valence I've never tried the interaction (self*valence). You might have to demean before computing the product On 8/14/2022 4:58 PM, Angela Fang wrote: External Email - Use Caution The two coding schemes are different because the second one does include the self*valence variable you?re talking about, whereas the first one doesn?t. I only included the 2nd offset because you suggested to someone else to include it (see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Kzjcs0NvggeCWK1kZl8-I-MFSs4rN_Hg2bVAtJOtXmUPa…<https://secure-web.cisco.com/1KSI9ZXHXrZ8C4oqRtPTT2v71_a-tcfPU0hEXz7rHdpuPX…> <https://secure-web.cisco.com/1dROBKZ9o4EJYvhHroZXaYPk9R6pjYchJGNg3Ad1pZOuYx… hRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>). If we don?t need it, would it just be 2 conditions, as follows? 1. SelfOffset 2. Self*ValenceSlope But then I?m not clear how to get the main effect of valence (brain regions that scale with increasing emotion valence, while holding self-relevance constant)? From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, August 14, 2022 at 1:37 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates Those look like they are the same coding scheme. What is different? You can only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an interaction. If you want an interaction you have to create a new variable which is SelfRating*ValenceRating. On 8/10/2022 2:38 PM, Angela Fang wrote: External Email - Use Caution Hello, Just re-sending my question below. If I have a variable with 2 levels (yes/no) and another variable that is continuous, based on this post (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Kzjcs0NvggeCWK1kZl8-I-MFSs4rN_Hg2bVAtJOtXmUPa…<https://secure-web.cisco.com/1KSI9ZXHXrZ8C4oqRtPTT2v71_a-tcfPU0hEXz7rHdpuPX…> <https://secure-web.cisco.com/1_Gtfo2yKt2DKNU7salt5D1ifrUCoKpSQ-Gd1yXJzCi_2-… 4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>), it sounds like I should code as follows: 1. SelfOffset 2. Self-ValenceSlope (would the weight in the 4th column reflect the value of self multiplied by the value of valence for this participant?) 3. NonSelfOffset 4. NonSelf-ValenceSlope If the other way of modifying the paradigm file is also acceptable to test the interaction (as I describe below), that would also be helpful to know. Thanks! Angela From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Fang <angfang(a)uw.edu><mailto:angfang@uw.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, August 1, 2022 at 4:35 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates External Email - Use Caution Hi Doug, Nevermind to my first question! I read this post (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1LGBuJxHHKSzwKD7PliizTf89PUwndluGzvlD1fEjVDbHY…<https://secure-web.cisco.com/1ImoRPx6jheuADIqdZK1GQajD1zmA_kwlqvN_DSHKmInHD…> <https://secure-web.cisco.com/1kImHf1vhX5JLuqrMAHPFz6QxGrndWwDqPfZKbay4rtc3D… archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>) and realized that we always include a subject-specific par file in each run for first-level analyses. However, I?m still confused about how to modify my paradigm file. I also need to model the trials of non-interest, so would it be as follows? 0 1 2.5 1.0 SelfOffset 0 2 2.5 1.0 SelfSlope (equal to subject?s rating of self-relevance) 0 3 2.5 1.0 ValenceOffset 0 4 2.5 3.0 ValenceSlope (equal to subject?s rating of valence) 2.5 0 2.5 1.0 FIXATION 5.0 1 2.5 1.0 SelfOffset 5.0 2 2.5 0 SelfSlope (equal to subject?s rating of self-relevance, in this case subject responded 0, or non-relevant) 5.0 3 2.5 1.0 ValenceOffset 5.0 4 2.5 2.0 ValenceSlope (equal to subject?s rating of valence) 7.5 5 2.5 1.0 OTHER Do these contrasts look correct to you? Self vs Fixation -a 1 -c 0 (main effect of self) Valence vs Fixation -a 3 -c 0 (main effect of valence) Self vs Valence -a 2 -a 4 (interaction between self x valence) Thank you so much for your help! Angela From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Fang <angfang(a)uw.edu><mailto:angfang@uw.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, July 28, 2022 at 1:02 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates Thanks Doug. This wiki page is extremely helpful. However, my question is about individual subject responses. I could see how you could include a summary (e.g., average) value of the parametric variable across subjects in your ?weight? column but it?s not clear to me how you could integrate individual subject responses to each word in the parametric modulation paradigm file? I?m imagining something like the FSGD file where a value is given for each subject, but for first-level analysis. We have a similar design as someone else who posted a similar question (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Kzjcs0NvggeCWK1kZl8-I-MFSs4rN_Hg2bVAtJOtXmUPa…<https://secure-web.cisco.com/1KSI9ZXHXrZ8C4oqRtPTT2v71_a-tcfPU0hEXz7rHdpuPX…> <https://secure-web.cisco.com/1Wr_kK45JmYzO8kdNVeLvoJZjzphTziDUSA67b8EMszmpn… ttps%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>). We have an event-related experiment presenting trait adjectives in terms of whether they describe themselves (SELF condition) or someone else (OTHER condition). We are interested in testing a 2x2 ANOVA to examine an interaction between self-relevance x emotional valence. Assuming you can?t integrate individual subject responses to each word in the paradigm file, would we set it up as follows? ?Usual? paradigm file: 0 1 2.5 1.0 SELF 2.5 0 2.5 1.0 FIXATION 5.0 1 2.5 1.0 SELF 7.5 2 2.5 1.0 OTHER Parametric modulation paradigm file: 0 1 2.5 1.0 SELFoffset 0 2 2.5 0.8 SELFslope 0 3 2.5 1.0 VALENCEoffset 0 4 2.5 2.0 VALENCEslope (where 0.8 reflects the percentage of time the word was endorsed as self-relevant and 2.0 is the average valence rating given for that word) And then create a contrast of 2 vs 4 to test the interaction? Would testing contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 vs 0 the main effect of valence? Thanks so much for your help! Angela From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, July 28, 2022 at 10:25 AM To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates Yes, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rFJQ0YeC1mTBGD5YbmaxaxlC_Ji0_fecqBr3-B9xpdMLv…<https://secure-web.cisco.com/15H9r2ZquFrm3-087noGOiU8bdud1WhXQ88PAmsvrBNcMG…> <https://secure-web.cisco.com/11YZPmGWkdn7MC0bWcIN8GddULibRexTsKKnjnVCN8548T… ulation> On 7/25/2022 6:56 PM, Angela Fang wrote: External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives are descriptive of themselves or not, and afterwards asked them to rate each trait word on emotional valence. Is it possible to include these individual level subjective ratings of emotional valence as covariates in the first level contrast in FSFAST? If so, how? Thanks, Angela --- Angela Fang, Ph.D. Assistant Professor Department of Psychology University of Washington Lab website: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NZFpiK7yuplLybIvSxfnqTa2P-KpLDkxN_dtmqCcGDGtU…<https://secure-web.cisco.com/1FxzbvHhIfbRqZ_QGItCfHrwmb08bZGcDsS3UZgOiVADE3…> <https://secure-web.cisco.com/1FdnYwRQVH4-QWyIacZwWj05HBBIz7pecKeBOQZlQYgQDZ… > Pronouns: she, her, hers _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Phmqmmpl9lmE_oOmrRpxz0_d8atG4Ra9iU54fm-P_Rz4D…<https://secure-web.cisco.com/1nhPClAJ8P_WZ1rYqP9mG4AIuKzwKjMzqlzORM9HTptNlo…> <https://secure-web.cisco.com/1BbiiI3KJ4a-I8lkVzs6CBlwBmP-_NBmWD8-3iiK4CIl5o… > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Phmqmmpl9lmE_oOmrRpxz0_d8atG4Ra9iU54fm-P_Rz4D…<https://secure-web.cisco.com/1nhPClAJ8P_WZ1rYqP9mG4AIuKzwKjMzqlzORM9HTptNlo…> <https://secure-web.cisco.com/1vYxoJ8LFQf32NMVHujqWx5q8LEOLRJrLZ8j-oC7o8Pwh-… > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Phmqmmpl9lmE_oOmrRpxz0_d8atG4Ra9iU54fm-P_Rz4D…<https://secure-web.cisco.com/1nhPClAJ8P_WZ1rYqP9mG4AIuKzwKjMzqlzORM9HTptNlo…> <https://secure-web.cisco.com/1kqNoZcL6GXHgxTbcaBrFfVBuiHD7XTt5ZlXkpkA4wFkrQ… > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1Phmqmmpl9lmE_oOmrRpxz0_d8atG4Ra9iU54fm-P_Rz4D…<https://secure-web.cisco.com/1nhPClAJ8P_WZ1rYqP9mG4AIuKzwKjMzqlzORM9HTptNlo…>

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dcmunpack
by O'Dor, Sarah,PHD 23 Sep '22

23 Sep '22

Good afternoon, Quick question about unpacking: The instructions I have from a previous staff member said to do this: In folder where files are going, type: unpacksdcmdir -src <location of scans> -targ . -scanonly scanout.txt So what I submit is: unpacksdcmdir -src /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -targ . -scanonly scanout.txt When I do that, it just makes the files: dicomdir.sumfile scanout.txt unpack.log I’m trying to use the dcmunpack command instead. From following the template on the website, I’ve been trying the following commands: [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -index-out dcm.index.dat {lots of other content here, so let’s skip to….} dcmunpack done [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -index-in dcm.index.dat -targ . ERROR: need input runs How should I specify input runs? Thanks, Sarah

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Fwd: Error
by Ahmad Khan 23 Sep '22

23 Sep '22

External Email - Use Caution Dear Free Surfer Development Team. I am using the recon -all command to compute the volume of different regions of the brain. I am running the free surfer version freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on a virtual box. I am getting the following errors and the log file is also attached with this email. *ERROR: mri_ca_register with non-zero status 137* Your timely response would be highly appreciated. Best Regards Dr. Ahmad Raza Khan (Ramalingaswami Fellow) Center of Bio-Medical Research (CBMR) SGPGI Campus, Raibareli Road Lucknow-226014, UP, INDIA

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Re: [Freesurfer] Error
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Hello Ahmed, Command terminated by signal 9 can mean you ran out of memory.  I would try allocating more memory to the VM.  But you may still run out of memory depending upon what is available on your machine. If you do not have to use 7.1.1 and can switch to using the newer 7.3.2 release, then for Ubuntu 20, we have a .deb file installer (https://secure-web.cisco.com/1X7NA_6gOlCGu2ju8c-dGWtwYTkO0F2UyQn6LX3rWhDeWj… or a tar archive (https://secure-web.cisco.com/1UYiwKeazHITmgtErAJKToWU57RsDIl-czevJWE_lnANvB…) which you try.  I would uninstall 7.1.1 if you are going to use 7.3.2 though.  Again, that may not help if available memory is the issue. - R. On Sep 23, 2022, at 02:04, Ahmad Khan <110ahmadkhan(a)gmail.com> wrote:        External Email - Use Caution         Dear Free Surfer Development Team.I am using the recon -all command to compute the volume of different regions of the brain. I am running the free surfer version freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on a virtual box. I am getting the following errors and the log file is also attached with this email. ERROR: mri_ca_register with non-zero status 137Your timely response would be highly appreciated.Best Regards Dr. Ahmad Raza Khan(Ramalingaswami Fellow)Center of Bio-Medical Research (CBMR)SGPGI Campus, Raibareli RoadLucknow-226014, UP, INDIA<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Running v7 with recon-all v6 files
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Hello Alexandra Please let us know if you are on an Intel or a newer Mac with an arm processor, e.g., M1, M2 chip.  You could send along a screen shot of what "About this Mac" displays. Per the "Important Note" at the bottom of the freesurfer release page, https://secure-web.cisco.com/1bbOhG1CjL59gEStW3FxyyS6evApjdBtrtnRNMXkTQqF0f…, you may not get exactly the same (floating point) results when running v6 on a different/newer version of MacOS. - R. On 9/22/22 09:36, Alexandra Brouillard (brouillard.alexandra(a)gmail.com) wrote:         External Email - Use Caution         Hi   I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ‘permission denied’ error when typing ‘$FREESURFER_HOME’ (but have the permissions/sudo). I also can’t open Freeview: by double clicking on the app, the GUI crashes, or by typing ‘freeview’ in the terminal I get a PETSC error.  According to some previous forum threads, I’m thinking of downloading the v7 but would like to validate that it’s OK when using recon-all v6 files.   Thank you for your support,   Alexandra   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1wXMF-HNnKPbJ6UCMl7zjaYS6CvQ0xP-EjJ9WxjSWmuVhO… 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1bQ9M6iur_iW-pPNsqXlrhmaSi_R4XGPHVen9gzb4NtkW_… <https://secure-web.cisco.com/1QEu65hJzFz0Qlr-f85ovtCCFPcEQTuVjkATuX8Dzuz3-aNImRz08NXygo1pKr2Wbp8Y7ERP6XX_QXuwwA7OQtL95Jy8KMvQkj8V15v6C3snSGsuYEymHIorCwk50lasrKb8M0DVESSb7lpsfhGW7Z8XrutrhY2vETqwYjoknqZ2L7coJdB9m0JwsRPxH88FkJaPyuapnujCIKZ0QiH7JLW_PxPUN1xjG8C0rI2ClwPd8PHXFdDo4ft_5ujxHY0YquA5UdKOwf3hc1himt1m2KKha9Xl8cwmMraWndDu5-S3ei8hubimZcdWjlXmybq7wVZ40Jt_OHoyghzrMyO1mZg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
by fsbuild 22 Sep '22

22 Sep '22

External Email - Use Caution I can check to see if there is a license in the Freesurfer v5 Ubuntu VM I mentioned in the previous email and send it to you to try.   But per my last email, I don’t know a way to decode an old license on newer versions of the OS where glibc has been updated short of re-compiling what decodes the license.   The most practical option may be to run FS 5.3 on a server that hosts an old version of Ubuntu that works with your existing license.   That can be done using a headless VM or container where the image runs off an SSD with a hefty amount of RAM assigned to it.  Ubuntu supports QEMU virtualization like most linux OS’s and I think you just install those packages from the linux repos.  For commercial software, VMware has enterprise level server hosting options for these kinds of tasks. - R. On Sep 22, 2022, at 06:25, Caspar Schwiedrzik <cschwiedrz(a)mail.rockefeller.edu> wrote:        External Email - Use Caution        Hi! Would it be possible to obtain a license file for Freesurfer v5.3 that is compatible with the glibc versions on newer Linux systems? That would go a long way in resolving our issues. Thank you, Caspar _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Longitudinal PET analysis
by Gomar, Jesus 22 Sep '22

22 Sep '22

External Email - Use Caution Hello Freesurfer developers, I am interested in analyzing PET data following a longitudinal design. I have co-registered each PET image to the closest MRI in time processed through the longitudinal stream. I have sampled each co-registered PET image time-point onto fsaverage surface via the individual's subject surface (mri_vol2surf). >From this point: 1. Is it possible to obtain spc (symmetrized percent change) using long_mris_slopes for each subject? 2. Is there a way to input the sampled surfaces into a qdec file for long_mris_slopes command? 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0. 2) Platform: Ubuntu 18,04.6 LTS 3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thank you! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
by Caspar Schwiedrzik 22 Sep '22

22 Sep '22

External Email - Use Caution Hi! Would it be possible to obtain a license file for Freesurfer v5.3 that is compatible with the glibc versions on newer Linux systems? That would go a long way in resolving our issues. Thank you, Caspar

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Three year postdoctoral fellowship in large-scale neuroimaging of thalamus and brainstem nuclei in brain disorders at the Norwegian Centre for Mental Disorders Research (NORMENT)
by Stener Nerland 22 Sep '22

22 Sep '22

External Email - Use Caution NORMENT runs a multicenter study involving hospital departments in Oslo and several research groups at the University of Oslo. The purpose of the programme is to study how biological/genetic, psychological and environmental factors contribute to mental and other brain disorders. We pursue diversity among our job applicants and encourage everyone to apply regardless of who you are and what background you have. Duties and responsibilities: Novel magnetic resonance imaging (MRI)-based tools will be used to investigate the structure of individual thalamic and brainstem nuclei in a large in-house multi-site sample of healthy controls (HCs; N>38,000) and participants with common brain disorders (N>5,900), including schizophrenia (SCZ; N>1,100) and bipolar disorders (BD; N>450). To determine how the thalamic and brainstem nuclei alterations affect cortical functioning, we will obtain electroencephalography (EEG)-based indices of cortical synaptic function and cortical oscillatory activity from patients and HCs with MRI (N>650). The overall goal of the study is to advance our understanding of 1) whether individual thalamic and brainstem nuclei are altered in common brain disorders, 2) how the nuclei alterations affect cortical functioning, and 3) if these alterations link to clinically relevant subgroups. The successful candidate will analyze and publish already collected clinical and MRI data and contribute to the ongoing data collection. Qualifications: Successful applicants must hold a PhD degree in neuroscience or equivalent, document experience in neuroimaging-based research, preferably from MRI- or EEG-based projects. Strong analytical and problem solving skills and attention to details are desirable. Personal skills will be emphasized. The candidate should be able to work independently and interactively in a team setting, be motivated and responsible, and be passionate about research. We can offer: An exciting research environment with a multidisciplinary profile and great opportunities for academic development. Attractive welfare and pension arrangements and a salary level in accordance with qualifications. For more information and to submit an application, please follow this link to the job announcement: https://secure-web.cisco.com/1yc_HfEpKe3vd6nOQKOBMCR6VMhZ8_qV6S4p8aHl4NWWOV…

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