Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

intrareg: Undefined variable
by miracle ozzoude 26 Sep '22

26 Sep '22

External Email - Use Caution Hello, I am trying to run TRACULA using FreeSurfer version7.2. I followed the instructions on the tutorial website for cross-sectional study with 1 scan (see link below). However, I keep getting "intrareg:Undefined variable" error whenever I run the first step "trac-all -prep -c tracula.file". I checked my config file and I did set intrareg = 3. Any suggestions on what the issue is/how to fix it? I have attached my config file in the email below, in addition to the log file. The participants' recon-all were processed using freesurfer v6.0 Many thanks, Paul

1 1

confirmation of processes/commands used in full processing pipeline
by Harriott, Emily M 26 Sep '22

26 Sep '22

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all doing well. I'm a second-year doctoral student (and beginner FreeSurfer user) trying to use FreeSurfer to segment gray and white matter in 90 T1 images of children/adolescents (with reading disorders, Neurofibromatosis type 1, and typically developing) for a project; I have two questions about processing these images, and I would be so very grateful to receive some thoughts/suggestions/advice etc. from some FreeSurfer experts such as yourselves. I ran recon-all on each of those 90 images, but one single run of recon-all left too much dura in the gray matter segmentation and too much white matter out of the white matter segmentation (the amount of white matter left out varied depending on the intensity contrast of each image). To fix the dura/gray matter issue, I re-ran recon-all using the -gcut flag and edited out by hand the remaining dura; this seemed to help. To fix the white matter issue, I tried adding control points and adding white matter voxels and re-running recon-all; this unfortunately did not seem to help, as control points led to worse segmentation and the added white matter voxels had minimal to no effect. So, after some experimentation, I have created a full processing pipeline to use on my data. But, before I apply it to all 90 images, I wanted to confirm with you all experts that this will 1) work and 2) do what I want it to do. Question 1: If I process my data in FS 7.2.0, can I go back and analyze it using QDEC in FS 6.0.0? Or do I have to process it in 6.0.0 to use QDEC? Question 2: Here is my pipeline (see below). Will this work? Will it do what I want it to do? Do you have any suggestions? I'm a beginner; is there anything I should be careful of or watch out for that I don't know about? After some experimentation on a subsample, this pipeline appears to work, but I really want to ensure it is doing what I want it to do and will do that consistently. For one subject.... I first run the initial recon-all (with some flags). $recon-all -i <input image> -s <subjID> -sd <subjects_dir> -wsthresh 10 -gcut -qcache Next, I open brainmask.mgz in FreeView and edit out the remaining dura mater by hand. When I save this new brainmask.mgz, I overwrite the old brainmask.mgz with this new edited brainmask.mgz. I then run multiple second iterations of recon-all, allowing me to use different seg-wlo thresholds (seg-wlo thresholds of 40, 50, 60, 70, 80, 90 are applied to each image). The multiple second iterations of recon-all are: $recon-all autorecon2 -s <subjID> -sd <subjects_90> -seg-wlo 90 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_80> -seg-wlo 80 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_70> -seg-wlo 70 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_60> -seg-wlo 60 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_50> -seg-wlo 50 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_40> -seg-wlo 40 -qcache (Note that I have 6 distinct subjects_?0 folders for 6 distinct seg-wlo values) In FreeView, I then visually assess the image/segmentation produced by each seg-wlo threshold to select the threshold that most optimally segmented the gray and white matter. I save the subject folder with the optimal seg-wlo threshold, as determined visually in FreeView by me, to a new subjects directory; this new subjects directory's folder is specified "SELECT". I now have measures of cortical thickness, surface area, and volume, but I also want measures of local gyrification index (LGI). With MATLAB 2022a active (I'm working on a large computing cluster, so I have to activate MATLAB/2022a as a module), I run the LGI recon-all. $recon-all -s <subjID> -sd <subjects_SELECT> -localGI -qcache I then obtain the measurements of LGI. To run this line, I also have a .bashrc file in my subjects_SELECT folder that has one line: MEASURE1 = pial_lgi. $recon-all -s <subjID> -sd <subjects_SELECT> -measure pial_lgi -qcache Then the data go into QDEC and I should be able to analyze from there. Any confirmations/denials, suggestions, or advice you all have would be so very greatly appreciated. Thank you so very much! Emily Harriott Doctoral Student, Vanderbilt University Nashville, TN

2 2

Fully funded postdoctoral fellowship in Ottawa, Canada
by Lauri Tuominen 26 Sep '22

26 Sep '22

External Email - Use Caution Drs. Lauri Tuominen and Sara Tremblay at the Institute of Mental Health Research in Ottawa are looking for a postdoctoral fellow. The candidate should have strong experimental skills in resting state fMRI to be able to develop and implement an fMRI protocol for targeting TMS in the treatment of major depressive disorder. The Institute of Mental Health Research in Ottawa hosts a Siemens mMR Biograph PET/MRI scanner, state-of-the-art TMS equipment, and excellent computing resources. The selected candidate will gain experience in conducting a randomized controlled trial, an opportunity to explore a range of questions using multimodal data including TMS, fMRI, and PET and have the opportunity to work with a diverse team of experts. For details, please visit: https://secure-web.cisco.com/1pBcLS2FQ9PAJwHQqnBym-wJFvufqJgyeD4wunEKVvgzfr… If you have questions regarding the position please send an email to Lauri Tuominen (lauri.tuominen(a)theroyal.ca)

1 0

SAMSEG - modification of the template files
by Mikolaj Pawlak 25 Sep '22

25 Sep '22

External Email - Use Caution Dear Freesurfers, I have been using samseg for a while and like it a lot. Thank you for this tool. How do you modify the template for this tool? Is there a guideline for this? I would like to divide Fluid_Inside_Eyes label to left and right and improve the bone information in the template. What is the procedure? thanks, Mikolaj Pawlak

2 7

Sclimbic segmentation error
by bar gen 25 Sep '22

25 Sep '22

External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. mri_sclimbic_seg --i /Users/mdbargen/Documents/control-T1 --o /Users/mdbargen/Documents/control-limbic --conform Segmenting image 1/68 Loaded input image from /Users/barisgenc/Documents/Kontrol-T1/Acar_Ebru-T1.nii.gz Traceback (most recent call last): File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 1048, in <module> main() File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 312, in main segmenter.process_files(**params) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 577, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 497, in segment conformed = self.preprocess(image) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 469, in preprocess print('The input image has resolution (%4.2f,%4.2f,%4.2f) mm, but 1mm-isotropic input is required.\n' TypeError: only size-1 arrays can be converted to Python scalars How can i solve this?

2 1

(no subject)
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Sorry if this is a repeat email from last night, but signal 9 can mean you ran out of memory.  You should try allocating more memory to the VM.. You could also try running the latest freesufer version = 7.3.2 which is compiled for Ubuntu 20 and you can get from, https://secure-web.cisco.com/1qqb_N_CupmU2BzFF50PfaJo-Ylza_cis45…  I would uninstall 7.1.1 if you are going to try 7.3.2, but a different version won’t make a difference if you are running short on available RAM. - R. On Sep 23, 2022, at 09:50, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:not sure what is going on. It received a kill signal (the 9 mentioned at the end). This often means that it was killed externally. Does this happen repeatedly? Does this happen on other subjects? How much memory did you allocate to your virtual box?On 9/23/2022 1:04 AM, Ahmad Khan 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_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/15PFLqzDL1HVPjQsEm2xIbfuOh37ckPLkKOr9B6nfzZplq… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

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

2 1

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…>

2 1

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

2 1

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

2 1

← Newer
1
2
3
4
5
6
7
...
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2022